{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"SINGLE\", technology = \"unknown\" and tissue_curation_coarse = \"Cardiovascular System\"", "rows": [[5879, "ERR1759701", "ERX1826022", "ERS1474296", "ERP020578", "PRJEB18632", "RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf", "E-MTAB-5323", "Transcriptome Analysis", "The aim of this analysis is to uncover novel  molecules synthesized and secreted from cardiomyocytes.", "ENA FIRST PUBLIC:2016 12 20|ENA LAST UPDATE:2016 12 15|ArrayExpress:E MTAB 5323", null, "Protocols: To obtain only cardiomyocytes from the heart  two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter  nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA  pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry  or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry  or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture's instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently  the sample was end repaired  dA tailed  adaptor ligated  and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs.", "Sample2", "SAMEA27136168", "Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute", "ENA first public:2016 12 20|ENA last update:2016 12 15|External Id:SAMEA27136168|INSDC center alias:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|INSDC center name:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|INSDC first public:2016 12 20T17:02:09Z|INSDC last update:2016 12 15T11:23:10Z|INSDC status:public|Submitter Id:E MTAB 5323:Sample2|broker name:ArrayExpress|cell type:cardiac myocyte|common name:zebrafish|developmental stage:72 hpf|genotype:Tgmyl7:actn2 tdEodncv44Tg|sample name:E MTAB 5323:Sample2", null, null, null, null, null, null, null, null, "Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf", "E MTAB 5323:Sample2 s", "Sample2 s", "RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf", "To obtain only cardiomyocytes from the heart  two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter  nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes.   Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA  pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry  or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry  or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture\u2019s instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently  the sample was end repaired  dA tailed  adaptor ligated  and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs.", "Experimental Factor: Tgmyl7:actn2 tdEodncv44Tg:genotype", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina MiSeq", null, "ERP020578", "Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf", "ENA FIRST PUBLIC:2016 12 20|ENA LAST UPDATE:2018 11 16", "mochizukis_lab_myl7_actn2tdEos_72h_01.fastq.gz", "fastq", 448234901.0, 6016977.0, "E MTAB 5323:Sample2", "0:74.50 1:0", "A:118923409;C:100586009;G:99987046;T:126071553;N:2666884", 74, 0, null, null, 118923409, 100586009, 99987046, 126071553, 2666884, "ERX1826022", "ERS1474296", "ERA776061", "Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|European Nucleotide Archive", "Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|European Nucleotide Archive", 1, 0.88465, null, 0.27583, null, 0.75398, null, 0.55917, null, 75, null, "B", null, "usable mapping rate", "illumina", "miseq", "full_length", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Japan", "2016-12-15", "Larval", "Larval", "Heart", "Cardiovascular System"], [5880, "ERR1759702", "ERX1826022", "ERS1474296", "ERP020578", "PRJEB18632", "RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf", "E-MTAB-5323", "Transcriptome Analysis", "The aim of this analysis is to uncover novel  molecules synthesized and secreted from cardiomyocytes.", "ENA FIRST PUBLIC:2016 12 20|ENA LAST UPDATE:2016 12 15|ArrayExpress:E MTAB 5323", null, "Protocols: To obtain only cardiomyocytes from the heart  two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter  nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA  pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry  or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry  or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture's instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently  the sample was end repaired  dA tailed  adaptor ligated  and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs.", "Sample2", "SAMEA27136168", "Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute", "ENA first public:2016 12 20|ENA last update:2016 12 15|External Id:SAMEA27136168|INSDC center alias:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|INSDC center name:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|INSDC first public:2016 12 20T17:02:09Z|INSDC last update:2016 12 15T11:23:10Z|INSDC status:public|Submitter Id:E MTAB 5323:Sample2|broker name:ArrayExpress|cell type:cardiac myocyte|common name:zebrafish|developmental stage:72 hpf|genotype:Tgmyl7:actn2 tdEodncv44Tg|sample name:E MTAB 5323:Sample2", null, null, null, null, null, null, null, null, "Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf", "E MTAB 5323:Sample2 s", "Sample2 s", "RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf", "To obtain only cardiomyocytes from the heart  two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter  nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes.   Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA  pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry  or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry  or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture\u2019s instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently  the sample was end repaired  dA tailed  adaptor ligated  and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs.", "Experimental Factor: Tgmyl7:actn2 tdEodncv44Tg:genotype", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina MiSeq", null, "ERP020578", "Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf", "ENA FIRST PUBLIC:2016 12 20|ENA LAST UPDATE:2018 11 16", "mochizukis_lab_myl7_actn2tdEos_72h_02.fastq.gz", "fastq", 448116860.0, 6016977.0, "E MTAB 5323:Sample2 1", "0:0 1:74.48", "A:127811460;C:99875207;G:106561979;T:113792335;N:75879", 0, 74, null, null, 127811460, 99875207, 106561979, 113792335, 75879, "ERX1826022", "ERS1474296", "ERA776061", "Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|European Nucleotide Archive", "Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|European Nucleotide Archive", 1, 0.91589, null, 0.2509, null, 0.79005, null, 0.54852, null, 75, null, "B", null, "usable mapping rate", "illumina", "miseq", "full_length", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Japan", "2016-12-15", "Larval", "Larval", "Heart", "Cardiovascular System"], [5881, "ERR1759699", "ERX1826021", "ERS1474295", "ERP020578", "PRJEB18632", "RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf", "E-MTAB-5323", "Transcriptome Analysis", "The aim of this analysis is to uncover novel  molecules synthesized and secreted from cardiomyocytes.", "ENA FIRST PUBLIC:2016 12 20|ENA LAST UPDATE:2016 12 15|ArrayExpress:E MTAB 5323", null, "Protocols: To obtain only cardiomyocytes from the heart  two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter  nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA  pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry  or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry  or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture's instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently  the sample was end repaired  dA tailed  adaptor ligated  and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs.", "Sample1", "SAMEA27135418", "Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute", "ENA first public:2016 12 20|ENA last update:2016 12 15|External Id:SAMEA27135418|INSDC center alias:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|INSDC center name:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|INSDC first public:2016 12 20T17:02:09Z|INSDC last update:2016 12 15T11:23:10Z|INSDC status:public|Submitter Id:E MTAB 5323:Sample1|broker name:ArrayExpress|cell type:cardiac myocyte|common name:zebrafish|developmental stage:72 hpf|genotype:Tgmyl7:Nls mCherryncv11Tg|sample name:E MTAB 5323:Sample1", null, null, null, null, null, null, null, null, "Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf", "E MTAB 5323:Sample1 s", "Sample1 s", "RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf", "To obtain only cardiomyocytes from the heart  two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter  nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes.   Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA  pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry  or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry  or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture\u2019s instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently  the sample was end repaired  dA tailed  adaptor ligated  and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs.", "Experimental Factor: Tgmyl7:Nls mCherryncv11Tg:genotype", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina MiSeq", null, "ERP020578", "Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf", "ENA FIRST PUBLIC:2016 12 20|ENA LAST UPDATE:2018 11 16", "mochizukis_lab_myl7_NLSmCherry_72h_01.fastq.gz", "fastq", 766363334.0, 10284347.0, "E MTAB 5323:Sample1", "0:74.52 1:0", "A:201960096;C:174999154;G:173403690;T:211341998;N:4658396", 74, 0, null, null, 201960096, 174999154, 173403690, 211341998, 4658396, "ERX1826021", "ERS1474295", "ERA776061", "Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|European Nucleotide Archive", "Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|European Nucleotide Archive", 1, 0.86003, null, 0.20554, null, 0.76301, null, 0.55753, null, 74, null, "B", null, "usable mapping rate", "illumina", "miseq", "full_length", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Japan", "2016-12-15", "Larval", "Larval", "Heart", "Cardiovascular System"], [5882, "ERR1759700", "ERX1826021", "ERS1474295", "ERP020578", "PRJEB18632", "RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf", "E-MTAB-5323", "Transcriptome Analysis", "The aim of this analysis is to uncover novel  molecules synthesized and secreted from cardiomyocytes.", "ENA FIRST PUBLIC:2016 12 20|ENA LAST UPDATE:2016 12 15|ArrayExpress:E MTAB 5323", null, "Protocols: To obtain only cardiomyocytes from the heart  two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter  nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes. Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA  pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry  or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry  or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture's instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently  the sample was end repaired  dA tailed  adaptor ligated  and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs.", "Sample1", "SAMEA27135418", "Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute", "ENA first public:2016 12 20|ENA last update:2016 12 15|External Id:SAMEA27135418|INSDC center alias:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|INSDC center name:Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|INSDC first public:2016 12 20T17:02:09Z|INSDC last update:2016 12 15T11:23:10Z|INSDC status:public|Submitter Id:E MTAB 5323:Sample1|broker name:ArrayExpress|cell type:cardiac myocyte|common name:zebrafish|developmental stage:72 hpf|genotype:Tgmyl7:Nls mCherryncv11Tg|sample name:E MTAB 5323:Sample1", null, null, null, null, null, null, null, null, "Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf", "E MTAB 5323:Sample1 s", "Sample1 s", "RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf", "To obtain only cardiomyocytes from the heart  two transgenic zebrafish lines were established; Tgmyl7:NLS mCherry and Tgmyl7:actn2 tdEos. Using cardiac myosin light chain myl7 promoter  nuclear localization signal conjugated monomeric Cherry or actinin alpha 2 conjugated tandem Eos was expressed in cardiomyocytes.   Hearts resected from Tgmyl7:NLS mCherry or Tgmyl7:actn2 tdEos larvae at 72 hpf were collected and digested with protease solution PBS with 5 mg/ml trypsin and 1 mM EDTA  pH 8.0 for 1 h. Digestion was terminated with stop solution PBS with 30% fetal bovine serum and 6 mL calcium chloride. mCherry  or tdEos positive cells were collected as cardiomyocytes using a FACS Aria III cell sorter BD Bioscience Total RNAs were prepared from mCherry  or tdEos positive cells using a NucleoSpin XS kit Macherey Nagel according to the manufacture\u2019s instruction. Reverse transcription RT and cDNA library preparation were performed with a SMARTer Ultra Low RNA kit Clontech. cDNA was fragmented with a Covaris S 220 instrument Covaris. Subsequently  the sample was end repaired  dA tailed  adaptor ligated  and then subjected to PCR by using a NEBNext DNA Library Preparation and NEBNext Multiplex oligos for Illumina New England BioLabs.", "Experimental Factor: Tgmyl7:Nls mCherryncv11Tg:genotype", "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "SINGLE", "ILLUMINA", "Illumina MiSeq", null, "ERP020578", "Illumina MiSeq sequencing; RNA Seq analyses of zebrafish cardiomyocytes at 72 hpf", "ENA FIRST PUBLIC:2016 12 20|ENA LAST UPDATE:2018 11 16", "mochizukis_lab_myl7_NLSmCHerry_72h_02.fastq.gz", "fastq", 766251339.0, 10284347.0, "E MTAB 5323:Sample1 1", "0:0 1:74.51", "A:214234414;C:174215653;G:180382062;T:197361982;N:57228", 0, 74, null, null, 214234414, 174215653, 180382062, 197361982, 57228, "ERX1826021", "ERS1474295", "ERA776061", "Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|European Nucleotide Archive", "Department of Cell Biology National Cerebral and Cardiovascular Center Research Institute|European Nucleotide Archive", 1, 0.87766, null, 0.21561, null, 0.77477, null, 0.53919, null, 73, null, "B", null, "usable mapping rate", "illumina", "miseq", "full_length", "poly_a", "nebnext", "bulk", "unknown", "unknown", null, "Japan", "2016-12-15", "Larval", "Larval", "Heart", "Cardiovascular System"], [10056, "ERR4691987", "ERX4613068", "ERS5216074", "ERP124560", "PRJEB40865", "RNA seq of zebrafish adult MCU mutant hearts", "ena-STUDY-UCLA-16-10-2020-22:30:44:295-390", "Other", "We generated a zebrafish mitochondrial calcium uniporter MCU mutant that is able to survive to maturity  but exhibits cardiac function and structure defects.  We used RNA seq to help understand the gene expression changes that occur in the adult MCU heart.", "ENA FIRST PUBLIC:2020 12 10|ENA LAST UPDATE:2020 10 16", null, null, "zebrafish adult heart RNA", "SAMEA7457891", "UCLA", "ENA FIRST PUBLIC:2020 12 10T17:06:02Z|ENA LAST UPDATE:2020 10 16T22:30:48Z|External Id:SAMEA7457891|INSDC center name:UCLA|INSDC first public:2020 12 10T17:06:02Z|INSDC last update:2020 10 16T22:30:48Z|INSDC status:public|Submitter Id:mcu mutant 2|common name:zebrafish|dev stage:adult|sample name:mcu mutant 2|scientific name:Danio rerio|tissue type:heart", null, null, null, null, null, null, null, null, "Illumina HiSeq 3000 sequencing", "ena EXPERIMENT UCLA 16 10 2020 22:30:43:819 4", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "ERP124560", "Illumina HiSeq 3000 sequencing", "ENA FIRST PUBLIC:2020 12 10|ENA LAST UPDATE:2020 10 21", "MCU_2.fastq.gz", "fastq", 1291626898.0, 35072619.0, "ena RUN UCLA 16 10 2020 22:30:43:819 4", "0:36.83 1:0", "A:364596432;C:305716590;G:295397140;T:324498501;N:1418235", 36, 0, null, null, 364596432, 305716590, 295397140, 324498501, 1418235, "ERX4613068", "ERS5216074", "ERA2987364", "European Nucleotide Archive", "University of California, Los Angeles, USA", 1, 0.93311, null, 0.08182, null, 0.75852, null, 0.54813, null, 37, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-10-16", "Adult", "Adult", "Heart", "Cardiovascular System"], [10057, "ERR4691986", "ERX4613067", "ERS5216073", "ERP124560", "PRJEB40865", "RNA seq of zebrafish adult MCU mutant hearts", "ena-STUDY-UCLA-16-10-2020-22:30:44:295-390", "Other", "We generated a zebrafish mitochondrial calcium uniporter MCU mutant that is able to survive to maturity  but exhibits cardiac function and structure defects.  We used RNA seq to help understand the gene expression changes that occur in the adult MCU heart.", "ENA FIRST PUBLIC:2020 12 10|ENA LAST UPDATE:2020 10 16", null, null, "zebrafish adult heart RNA", "SAMEA7457890", "UCLA", "ENA FIRST PUBLIC:2020 12 10T17:06:02Z|ENA LAST UPDATE:2020 10 16T22:30:48Z|External Id:SAMEA7457890|INSDC center name:UCLA|INSDC first public:2020 12 10T17:06:02Z|INSDC last update:2020 10 16T22:30:48Z|INSDC status:public|Submitter Id:mcu mutant 1|common name:zebrafish|dev stage:adult|sample name:mcu mutant 1|scientific name:Danio rerio|tissue type:heart", null, null, null, null, null, null, null, null, "Illumina HiSeq 3000 sequencing", "ena EXPERIMENT UCLA 16 10 2020 22:30:43:819 3", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "ERP124560", "Illumina HiSeq 3000 sequencing", "ENA FIRST PUBLIC:2020 12 10|ENA LAST UPDATE:2020 10 21", "MCU_1.fastq.gz", "fastq", 1236033124.0, 33559740.0, "ena RUN UCLA 16 10 2020 22:30:43:819 3", "0:36.83 1:0", "A:348518065;C:293502111;G:279181983;T:313506799;N:1324166", 36, 0, null, null, 348518065, 293502111, 279181983, 313506799, 1324166, "ERX4613067", "ERS5216073", "ERA2987364", "European Nucleotide Archive", "University of California, Los Angeles, USA", 1, 0.92798, null, 0.07907, null, 0.7697, null, 0.5488, null, 37, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-10-16", "Adult", "Adult", "Heart", "Cardiovascular System"], [10058, "ERR4691985", "ERX4613066", "ERS5216072", "ERP124560", "PRJEB40865", "RNA seq of zebrafish adult MCU mutant hearts", "ena-STUDY-UCLA-16-10-2020-22:30:44:295-390", "Other", "We generated a zebrafish mitochondrial calcium uniporter MCU mutant that is able to survive to maturity  but exhibits cardiac function and structure defects.  We used RNA seq to help understand the gene expression changes that occur in the adult MCU heart.", "ENA FIRST PUBLIC:2020 12 10|ENA LAST UPDATE:2020 10 16", null, null, "zebrafish adult heart RNA", "SAMEA7457889", "UCLA", "ENA FIRST PUBLIC:2020 12 10T17:06:02Z|ENA LAST UPDATE:2020 10 16T22:30:48Z|External Id:SAMEA7457889|INSDC center name:UCLA|INSDC first public:2020 12 10T17:06:02Z|INSDC last update:2020 10 16T22:30:48Z|INSDC status:public|Submitter Id:wildtype 2|common name:zebrafish|dev stage:adult|sample name:wildtype 2|scientific name:Danio rerio|tissue type:heart", null, null, null, null, null, null, null, null, "Illumina HiSeq 3000 sequencing", "ena EXPERIMENT UCLA 16 10 2020 22:30:43:819 2", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "ERP124560", "Illumina HiSeq 3000 sequencing", "ENA FIRST PUBLIC:2020 12 10|ENA LAST UPDATE:2020 10 21", "WT_2.fastq.gz", "fastq", 1180831209.0, 32069533.0, "ena RUN UCLA 16 10 2020 22:30:43:819 2", "0:36.82 1:0", "A:328604642;C:281065336;G:278743466;T:291039015;N:1378750", 36, 0, null, null, 328604642, 281065336, 278743466, 291039015, 1378750, "ERX4613066", "ERS5216072", "ERA2987364", "European Nucleotide Archive", "University of California, Los Angeles, USA", 1, 0.92319, null, 0.08946, null, 0.75706, null, 0.49996, null, 37, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-10-16", "Adult", "Adult", "Heart", "Cardiovascular System"], [10059, "ERR4691984", "ERX4613065", "ERS5216071", "ERP124560", "PRJEB40865", "RNA seq of zebrafish adult MCU mutant hearts", "ena-STUDY-UCLA-16-10-2020-22:30:44:295-390", "Other", "We generated a zebrafish mitochondrial calcium uniporter MCU mutant that is able to survive to maturity  but exhibits cardiac function and structure defects.  We used RNA seq to help understand the gene expression changes that occur in the adult MCU heart.", "ENA FIRST PUBLIC:2020 12 10|ENA LAST UPDATE:2020 10 16", null, null, "zebrafish adult heart RNA", "SAMEA7457888", "UCLA", "ENA FIRST PUBLIC:2020 12 10T17:06:02Z|ENA LAST UPDATE:2020 10 16T22:30:48Z|External Id:SAMEA7457888|INSDC center name:UCLA|INSDC first public:2020 12 10T17:06:02Z|INSDC last update:2020 10 16T22:30:48Z|INSDC status:public|Submitter Id:wildtype 1|common name:zebrafish|dev stage:adult|sample name:wildtype 1|scientific name:Danio rerio|tissue type:heart", null, null, null, null, null, null, null, null, "Illumina HiSeq 3000 sequencing", "ena EXPERIMENT UCLA 16 10 2020 22:30:43:819 1", "unspecified", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "ERP124560", "Illumina HiSeq 3000 sequencing", "ENA FIRST PUBLIC:2020 12 10|ENA LAST UPDATE:2020 10 21", "WT_1.fastq.gz", "fastq", 1428414407.0, 38793098.0, "ena RUN UCLA 16 10 2020 22:30:43:819 1", "0:36.82 1:0", "A:398925739;C:338731211;G:333527196;T:355553981;N:1676280", 36, 0, null, null, 398925739, 338731211, 333527196, 355553981, 1676280, "ERX4613065", "ERS5216071", "ERA2987364", "European Nucleotide Archive", "University of California, Los Angeles, USA", 1, 0.92407, null, 0.08758, null, 0.75726, null, 0.4969, null, 37, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "unknown", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-10-16", "Adult", "Adult", "Heart", "Cardiovascular System"], [25170, "SRR25661605", "SRX21387413", "SRS18627977", "SRP455520", "PRJNA1006302", "The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes", "GSE241049", "Transcriptome Analysis", "To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.", null, "pubmed:39658721", null, "hand2 FLD+/? 20 hpf CMs rep3", "GSM7714404", null, "source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 mutants|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing", "hand2 FLD+/? 20 hpf CMs rep3", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter \u201c\u2013outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of \u00b11.5 log2\u2009\u00b1\u20090.59  a maximum Benjamini\u2013Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts", "embryonic heart", null, "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 mutants|treatment:sorted cells by FACS", "GSM7714404", "GSM7714404: hand2 FLD+/? 20 hpf CMs rep3; Danio rerio; RNA Seq", "GSM7714404 r1", "GSM7714404", "1", "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP455520", null, "loader:fastq load.py", "E22_3458_Yanli_HT_Lib_WT_het_3_R1.fastq.gz", "fastq", 2441736984.0, 34141777.0, "GSM7714404 r1", "0:71.52", "A:706186414;C:496261994;G:526176364;T:713112212;N:0", 71, null, null, null, 706186414, 496261994, 526176364, 713112212, 0, "SRX21387413", "SRS18627977", "SRA1694205", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.9026, null, 0.15816, null, 0.76278, null, 0.44042, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2023-08-17", "Segmentation", "Embryo", "Heart", "Cardiovascular System"], [25171, "SRR25661606", "SRX21387412", "SRS18627976", "SRP455520", "PRJNA1006302", "The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes", "GSE241049", "Transcriptome Analysis", "To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.", null, "pubmed:39658721", null, "hand2 FLD+/? 20 hpf CMs rep2", "GSM7714403", null, "source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 mutants|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing", "hand2 FLD+/? 20 hpf CMs rep2", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter \u201c\u2013outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of \u00b11.5 log2\u2009\u00b1\u20090.59  a maximum Benjamini\u2013Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts", "embryonic heart", null, "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 mutants|treatment:sorted cells by FACS", "GSM7714403", "GSM7714403: hand2 FLD+/? 20 hpf CMs rep2; Danio rerio; RNA Seq", "GSM7714403 r1", "GSM7714403", "1", "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP455520", null, "loader:fastq load.py", "E22_3458_Yanli_HT_Lib_WT_het_2_R1.fastq.gz", "fastq", 2185611269.0, 30558084.0, "GSM7714403 r1", "0:71.52", "A:612617675;C:458632518;G:474458738;T:639902338;N:0", 71, null, null, null, 612617675, 458632518, 474458738, 639902338, 0, "SRX21387412", "SRS18627976", "SRA1694205", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.90042, null, 0.14005, null, 0.75424, null, 0.44277, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2023-08-17", "Segmentation", "Embryo", "Heart", "Cardiovascular System"], [25172, "SRR25661607", "SRX21387411", "SRS18627975", "SRP455520", "PRJNA1006302", "The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes", "GSE241049", "Transcriptome Analysis", "To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.", null, "pubmed:39658721", null, "hand2 FLD+/? 20 hpf CMs rep1", "GSM7714402", null, "source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 mutants|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing", "hand2 FLD+/? 20 hpf CMs rep1", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter \u201c\u2013outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of \u00b11.5 log2\u2009\u00b1\u20090.59  a maximum Benjamini\u2013Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts", "embryonic heart", null, "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 mutants|treatment:sorted cells by FACS", "GSM7714402", "GSM7714402: hand2 FLD+/? 20 hpf CMs rep1; Danio rerio; RNA Seq", "GSM7714402 r1", "GSM7714402", "1", "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP455520", null, "loader:fastq load.py", "E22_3458_Yanli_HT_Lib_WT_het_1_R1.fastq.gz", "fastq", 2291884894.0, 32043147.0, "GSM7714402 r1", "0:71.52", "A:635094975;C:489594953;G:499909828;T:667285138;N:0", 71, null, null, null, 635094975, 489594953, 499909828, 667285138, 0, "SRX21387411", "SRS18627975", "SRA1694205", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.90883, null, 0.14288, null, 0.75331, null, 0.44459, null, 71, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2023-08-17", "Segmentation", "Embryo", "Heart", "Cardiovascular System"], [25173, "SRR25661608", "SRX21387410", "SRS18627974", "SRP455520", "PRJNA1006302", "The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes", "GSE241049", "Transcriptome Analysis", "To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.", null, "pubmed:39658721", null, "WT 20 hpf CMs rep3", "GSM7714401", null, "source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 OE|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing", "WT 20 hpf CMs rep3", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter \u201c\u2013outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of \u00b11.5 log2\u2009\u00b1\u20090.59  a maximum Benjamini\u2013Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts", "embryonic heart", null, "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 OE|treatment:sorted cells by FACS", "GSM7714401", "GSM7714401: WT 20 hpf CMs rep3; Danio rerio; RNA Seq", "GSM7714401 r1", "GSM7714401", "1", "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP455520", null, "loader:fastq load.py", "E22_3458_Yanli_HT_Lib_WT_CMs_3_R1.fastq.gz", "fastq", 2268251602.0, 31717610.0, "GSM7714401 r1", "0:71.51", "A:637196241;C:477782543;G:497683941;T:655588877;N:0", 71, null, null, null, 637196241, 477782543, 497683941, 655588877, 0, "SRX21387410", "SRS18627974", "SRA1694205", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.90026, null, 0.13291, null, 0.78707, null, 0.40811, null, 71, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2023-08-17", "Segmentation", "Embryo", "Heart", "Cardiovascular System"], [25174, "SRR25661609", "SRX21387409", "SRS18627973", "SRP455520", "PRJNA1006302", "The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes", "GSE241049", "Transcriptome Analysis", "To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.", null, "pubmed:39658721", null, "WT 20 hpf CMs rep2", "GSM7714400", null, "source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 OE|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing", "WT 20 hpf CMs rep2", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter \u201c\u2013outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of \u00b11.5 log2\u2009\u00b1\u20090.59  a maximum Benjamini\u2013Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts", "embryonic heart", null, "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 OE|treatment:sorted cells by FACS", "GSM7714400", "GSM7714400: WT 20 hpf CMs rep2; Danio rerio; RNA Seq", "GSM7714400 r1", "GSM7714400", "1", "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP455520", null, "loader:fastq load.py", "E22_3458_Yanli_HT_Lib_WT_CMs_2_R1.fastq.gz", "fastq", 2195524610.0, 30700033.0, "GSM7714400 r1", "0:71.52", "A:615401741;C:462686936;G:481135567;T:636300366;N:0", 71, null, null, null, 615401741, 462686936, 481135567, 636300366, 0, "SRX21387409", "SRS18627973", "SRA1694205", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.90323, null, 0.1476, null, 0.78744, null, 0.41728, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2023-08-17", "Segmentation", "Embryo", "Heart", "Cardiovascular System"], [25175, "SRR25661610", "SRX21387408", "SRS18627972", "SRP455520", "PRJNA1006302", "The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes", "GSE241049", "Transcriptome Analysis", "To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.", null, "pubmed:39658721", null, "WT 20 hpf CMs rep1", "GSM7714399", null, "source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 OE|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing", "WT 20 hpf CMs rep1", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter \u201c\u2013outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of \u00b11.5 log2\u2009\u00b1\u20090.59  a maximum Benjamini\u2013Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts", "embryonic heart", null, "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 OE|treatment:sorted cells by FACS", "GSM7714399", "GSM7714399: WT 20 hpf CMs rep1; Danio rerio; RNA Seq", "GSM7714399 r1", "GSM7714399", "1", "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP455520", null, "loader:fastq load.py", "E22_3458_Yanli_HT_Lib_WT_CMs_1_R1.fastq.gz", "fastq", 2258160684.0, 31576661.0, "GSM7714399 r1", "0:71.51", "A:641254288;C:471580136;G:491501482;T:653824778;N:0", 71, null, null, null, 641254288, 471580136, 491501482, 653824778, 0, "SRX21387408", "SRS18627972", "SRA1694205", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.9, null, 0.13993, null, 0.78445, null, 0.40575, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2023-08-17", "Segmentation", "Embryo", "Heart", "Cardiovascular System"], [25176, "SRR25661611", "SRX21387407", "SRS18627971", "SRP455520", "PRJNA1006302", "The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes", "GSE241049", "Transcriptome Analysis", "To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.", null, "pubmed:39658721", null, "hand2 OE 20 hpf CMs rep3", "GSM7714398", null, "source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:overexpression hand2 in myocardium|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing", "hand2 OE 20 hpf CMs rep3", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter \u201c\u2013outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of \u00b11.5 log2\u2009\u00b1\u20090.59  a maximum Benjamini\u2013Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts", "embryonic heart", null, "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "tissue:embryonic heart|cell type:cardiomyocytes|genotype:overexpression hand2 in myocardium|treatment:sorted cells by FACS", "GSM7714398", "GSM7714398: hand2 OE 20 hpf CMs rep3; Danio rerio; RNA Seq", "GSM7714398 r1", "GSM7714398", "1", "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP455520", null, "loader:fastq load.py", "E22_3458_Yanli_HT_Lib_OE_CMs_3_R1.fastq.gz", "fastq", 1886569909.0, 26380170.0, "GSM7714398 r1", "0:71.51", "A:534874421;C:392168718;G:411533838;T:547992932;N:0", 71, null, null, null, 534874421, 392168718, 411533838, 547992932, 0, "SRX21387407", "SRS18627971", "SRA1694205", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.89968, null, 0.14763, null, 0.77881, null, 0.42601, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2023-08-17", "Segmentation", "Embryo", "Heart", "Cardiovascular System"], [25177, "SRR25661612", "SRX21387406", "SRS18627970", "SRP455520", "PRJNA1006302", "The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes", "GSE241049", "Transcriptome Analysis", "To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.", null, "pubmed:39658721", null, "hand2 OE 20 hpf CMs rep2", "GSM7714397", null, "source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:overexpression hand2 in myocardium|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing", "hand2 OE 20 hpf CMs rep2", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter \u201c\u2013outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of \u00b11.5 log2\u2009\u00b1\u20090.59  a maximum Benjamini\u2013Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts", "embryonic heart", null, "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "tissue:embryonic heart|cell type:cardiomyocytes|genotype:overexpression hand2 in myocardium|treatment:sorted cells by FACS", "GSM7714397", "GSM7714397: hand2 OE 20 hpf CMs rep2; Danio rerio; RNA Seq", "GSM7714397 r1", "GSM7714397", "1", "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP455520", null, "loader:fastq load.py", "E22_3458_Yanli_HT_Lib_OE_CMs_2_R1.fastq.gz", "fastq", 2197151812.0, 30722639.0, "GSM7714397 r1", "0:71.52", "A:617116635;C:461951919;G:481371246;T:636712012;N:0", 71, null, null, null, 617116635, 461951919, 481371246, 636712012, 0, "SRX21387406", "SRS18627970", "SRA1694205", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.90877, null, 0.14744, null, 0.77191, null, 0.42845, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2023-08-17", "Segmentation", "Embryo", "Heart", "Cardiovascular System"], [25178, "SRR25661613", "SRX21387405", "SRS18627969", "SRP455520", "PRJNA1006302", "The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes", "GSE241049", "Transcriptome Analysis", "To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.", null, "pubmed:39658721", null, "hand2 OE 20 hpf CMs rep1", "GSM7714396", null, "source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:overexpression hand2 in myocardium|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing", "hand2 OE 20 hpf CMs rep1", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter \u201c\u2013outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of \u00b11.5 log2\u2009\u00b1\u20090.59  a maximum Benjamini\u2013Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts", "embryonic heart", null, "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "tissue:embryonic heart|cell type:cardiomyocytes|genotype:overexpression hand2 in myocardium|treatment:sorted cells by FACS", "GSM7714396", "GSM7714396: hand2 OE 20 hpf CMs rep1; Danio rerio; RNA Seq", "GSM7714396 r1", "GSM7714396", "1", "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP455520", null, "loader:fastq load.py", "E22_3458_Yanli_HT_Lib_OE_CMs_1_R1.fastq.gz", "fastq", 1773398936.0, 24797998.0, "GSM7714396 r1", "0:71.51", "A:495618212;C:375438077;G:390377060;T:511965587;N:0", 71, null, null, null, 495618212, 375438077, 390377060, 511965587, 0, "SRX21387405", "SRS18627969", "SRA1694205", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.90769, null, 0.1387, null, 0.7768, null, 0.42096, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2023-08-17", "Segmentation", "Embryo", "Heart", "Cardiovascular System"], [25179, "SRR25661614", "SRX21387404", "SRS18627968", "SRP455520", "PRJNA1006302", "The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes", "GSE241049", "Transcriptome Analysis", "To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.", null, "pubmed:39658721", null, "hand2 FLD /  20 hpf CMs rep3", "GSM7714395", null, "source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:hand2 mutant|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing", "hand2 FLD /  20 hpf CMs rep3", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter \u201c\u2013outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of \u00b11.5 log2\u2009\u00b1\u20090.59  a maximum Benjamini\u2013Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts", "embryonic heart", null, "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "tissue:embryonic heart|cell type:cardiomyocytes|genotype:hand2 mutant|treatment:sorted cells by FACS", "GSM7714395", "GSM7714395: hand2 FLD /  20 hpf CMs rep3; Danio rerio; RNA Seq", "GSM7714395 r1", "GSM7714395", "1", "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP455520", null, "loader:fastq load.py", "E22_3458_Yanli_HT_Lib_Mut_3_R1.fastq.gz", "fastq", 2179400259.0, 30471965.0, "GSM7714395 r1", "0:71.52", "A:600555691;C:468535203;G:483122661;T:627186704;N:0", 71, null, null, null, 600555691, 468535203, 483122661, 627186704, 0, "SRX21387404", "SRS18627968", "SRA1694205", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.91581, null, 0.12256, null, 0.75209, null, 0.43413, null, 71, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2023-08-17", "Segmentation", "Embryo", "Heart", "Cardiovascular System"], [25180, "SRR25661615", "SRX21387403", "SRS18627967", "SRP455520", "PRJNA1006302", "The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes", "GSE241049", "Transcriptome Analysis", "To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.", null, "pubmed:39658721", null, "hand2 FLD /  20 hpf CMs rep2", "GSM7714394", null, "source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:hand2 mutant|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing", "hand2 FLD /  20 hpf CMs rep2", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter \u201c\u2013outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of \u00b11.5 log2\u2009\u00b1\u20090.59  a maximum Benjamini\u2013Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts", "embryonic heart", null, "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "tissue:embryonic heart|cell type:cardiomyocytes|genotype:hand2 mutant|treatment:sorted cells by FACS", "GSM7714394", "GSM7714394: hand2 FLD /  20 hpf CMs rep2; Danio rerio; RNA Seq", "GSM7714394 r1", "GSM7714394", "1", "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP455520", null, "loader:fastq load.py", "E22_3458_Yanli_HT_Lib_Mut_2_R1.fastq.gz", "fastq", 2340991168.0, 32733068.0, "GSM7714394 r1", "0:71.52", "A:647423337;C:500120073;G:514803152;T:678644606;N:0", 71, null, null, null, 647423337, 500120073, 514803152, 678644606, 0, "SRX21387403", "SRS18627967", "SRA1694205", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.91231, null, 0.12561, null, 0.75118, null, 0.44445, null, 71, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2023-08-17", "Segmentation", "Embryo", "Heart", "Cardiovascular System"], [25181, "SRR25661616", "SRX21387402", "SRS18627966", "SRP455520", "PRJNA1006302", "The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes", "GSE241049", "Transcriptome Analysis", "To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.", null, "pubmed:39658721", null, "hand2 FLD /  20 hpf CMs rep1", "GSM7714393", null, "source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:hand2 mutant|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing", "hand2 FLD /  20 hpf CMs rep1", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter \u201c\u2013outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of \u00b11.5 log2\u2009\u00b1\u20090.59  a maximum Benjamini\u2013Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts", "embryonic heart", null, "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "tissue:embryonic heart|cell type:cardiomyocytes|genotype:hand2 mutant|treatment:sorted cells by FACS", "GSM7714393", "GSM7714393: hand2 FLD /  20 hpf CMs rep1; Danio rerio; RNA Seq", "GSM7714393 r1", "GSM7714393", "1", "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP455520", null, "loader:fastq load.py", "E22_3458_Yanli_HT_Lib_Mut_1_R1.fastq.gz", "fastq", 2727863036.0, 38140997.0, "GSM7714393 r1", "0:71.52", "A:760867462;C:577539041;G:596986102;T:792470431;N:0", 71, null, null, null, 760867462, 577539041, 596986102, 792470431, 0, "SRX21387402", "SRS18627966", "SRA1694205", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.91175, null, 0.1342, null, 0.75282, null, 0.44063, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2023-08-17", "Segmentation", "Embryo", "Heart", "Cardiovascular System"], [29086, "SRR27015250", "SRX22707800", "SRS19700101", "SRP475323", "PRJNA1047551", "Identification of genes important during atrial myocardial morphogenesis", "GSE249149", "Transcriptome Analysis", "Atrial cardiomyocytes undergo complex cellular behaviours post 72 hpf to build muscle structures.  We aimed to identify the genes involved during this process  and therefore we seqeunced the RNA from 48 hpf and 72 hpf atrial cardiomyocytes to uncover changes in the transcirptome that might regulate or trigger atrial morphogenesis post 72 hpf. Overall design: Comparative gene expression profiling analysis of RNA seq data for 48 hpf and 72 hpf wild type zebrafish atrial cardiomyocytes.", null, "pubmed:39289341", null, "Wild type zebrafish atrial cardiomyocytes  72 hpf  rep 3", "GSM7927521", null, "source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocyte|genotype:wild type|treatment:72 hpf loc name:missing|collection date:missing", "Wild type zebrafish atrial cardiomyocytes  72 hpf  rep 3", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Dobin et al.  STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Assembly: danRer11 Supplementary files format and content: count matrix", "embryonic heart", null, "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "tissue:embryonic heart|cell type:cardiomyocyte|genotype:wild type|treatment:72 hpf", "GSM7927521", "GSM7927521: Wild type zebrafish atrial cardiomyocytes  72 hpf  rep 3; Danio rerio; RNA Seq", "GSM7927521 r1", "GSM7927521", "1", "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP475323", null, "loader:fastq load.py", "dst226_zbrf_clt___ACrdmct-age___72h_b03_t01_m01_R1.fastq.gz", "fastq", 1709509823.0, 28403358.0, "GSM7927521 r1", "0:60.19", "A:400293032;C:330429588;G:326652799;T:383291002;N:268843402", 60, null, null, null, 400293032, 330429588, 326652799, 383291002, 268843402, "SRX22707800", "SRS19700101", "SRA1761360", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.90079, null, 0.0827, null, 0.81406, null, 0.64557, null, 35, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2023-12-01", "Larval", "Larval", "Heart", "Cardiovascular System"], [29087, "SRR27015251", "SRX22707799", "SRS19700100", "SRP475323", "PRJNA1047551", "Identification of genes important during atrial myocardial morphogenesis", "GSE249149", "Transcriptome Analysis", "Atrial cardiomyocytes undergo complex cellular behaviours post 72 hpf to build muscle structures.  We aimed to identify the genes involved during this process  and therefore we seqeunced the RNA from 48 hpf and 72 hpf atrial cardiomyocytes to uncover changes in the transcirptome that might regulate or trigger atrial morphogenesis post 72 hpf. Overall design: Comparative gene expression profiling analysis of RNA seq data for 48 hpf and 72 hpf wild type zebrafish atrial cardiomyocytes.", null, "pubmed:39289341", null, "Wild type zebrafish atrial cardiomyocytes  72 hpf  rep 2", "GSM7927520", null, "source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocyte|genotype:wild type|treatment:72 hpf loc name:missing|collection date:missing", "Wild type zebrafish atrial cardiomyocytes  72 hpf  rep 2", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Dobin et al.  STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Assembly: danRer11 Supplementary files format and content: count matrix", "embryonic heart", null, "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "tissue:embryonic heart|cell type:cardiomyocyte|genotype:wild type|treatment:72 hpf", "GSM7927520", "GSM7927520: Wild type zebrafish atrial cardiomyocytes  72 hpf  rep 2; Danio rerio; RNA Seq", "GSM7927520 r1", "GSM7927520", "1", "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP475323", null, "loader:fastq load.py", "dst226_zbrf_clt___ACrdmct-age___72h_b02_t01_m01_R1.fastq.gz", "fastq", 1740891025.0, 28211981.0, "GSM7927520 r1", "0:61.71", "A:419094150;C:347792831;G:345450108;T:407537501;N:221016435", 61, null, null, null, 419094150, 347792831, 345450108, 407537501, 221016435, "SRX22707799", "SRS19700100", "SRA1761360", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.90091, null, 0.13293, null, 0.78464, null, 0.54281, null, 69, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2023-12-01", "Larval", "Larval", "Heart", "Cardiovascular System"], [29088, "SRR27015252", "SRX22707798", "SRS19700099", "SRP475323", "PRJNA1047551", "Identification of genes important during atrial myocardial morphogenesis", "GSE249149", "Transcriptome Analysis", "Atrial cardiomyocytes undergo complex cellular behaviours post 72 hpf to build muscle structures.  We aimed to identify the genes involved during this process  and therefore we seqeunced the RNA from 48 hpf and 72 hpf atrial cardiomyocytes to uncover changes in the transcirptome that might regulate or trigger atrial morphogenesis post 72 hpf. Overall design: Comparative gene expression profiling analysis of RNA seq data for 48 hpf and 72 hpf wild type zebrafish atrial cardiomyocytes.", null, "pubmed:39289341", null, "Wild type zebrafish atrial cardiomyocytes  72 hpf  rep 1", "GSM7927519", null, "source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocyte|genotype:wild type|treatment:72 hpf loc name:missing|collection date:missing", "Wild type zebrafish atrial cardiomyocytes  72 hpf  rep 1", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Dobin et al.  STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Assembly: danRer11 Supplementary files format and content: count matrix", "embryonic heart", null, "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "tissue:embryonic heart|cell type:cardiomyocyte|genotype:wild type|treatment:72 hpf", "GSM7927519", "GSM7927519: Wild type zebrafish atrial cardiomyocytes  72 hpf  rep 1; Danio rerio; RNA Seq", "GSM7927519 r1", "GSM7927519", "1", "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP475323", null, "loader:fastq load.py", "dst226_zbrf_clt___ACrdmct-age___72h_b01_t01_m01_R1.fastq.gz", "fastq", 1930552948.0, 30996774.0, "GSM7927519 r1", "0:62.28", "A:468769814;C:389869994;G:387622687;T:454801262;N:229489191", 62, null, null, null, 468769814, 389869994, 387622687, 454801262, 229489191, "SRX22707798", "SRS19700099", "SRA1761360", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.90465, null, 0.10656, null, 0.79586, null, 0.55674, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2023-12-01", "Larval", "Larval", "Heart", "Cardiovascular System"], [29089, "SRR27015253", "SRX22707797", "SRS19700098", "SRP475323", "PRJNA1047551", "Identification of genes important during atrial myocardial morphogenesis", "GSE249149", "Transcriptome Analysis", "Atrial cardiomyocytes undergo complex cellular behaviours post 72 hpf to build muscle structures.  We aimed to identify the genes involved during this process  and therefore we seqeunced the RNA from 48 hpf and 72 hpf atrial cardiomyocytes to uncover changes in the transcirptome that might regulate or trigger atrial morphogenesis post 72 hpf. Overall design: Comparative gene expression profiling analysis of RNA seq data for 48 hpf and 72 hpf wild type zebrafish atrial cardiomyocytes.", null, "pubmed:39289341", null, "Wild type zebrafish atrial cardiomyocytes  48 hpf  rep 3", "GSM7927518", null, "source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocyte|genotype:wild type|treatment:48 hpf loc name:missing|collection date:missing", "Wild type zebrafish atrial cardiomyocytes  48 hpf  rep 3", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Dobin et al.  STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Assembly: danRer11 Supplementary files format and content: count matrix", "embryonic heart", null, "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "tissue:embryonic heart|cell type:cardiomyocyte|genotype:wild type|treatment:48 hpf", "GSM7927518", "GSM7927518: Wild type zebrafish atrial cardiomyocytes  48 hpf  rep 3; Danio rerio; RNA Seq", "GSM7927518 r1", "GSM7927518", "1", "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP475323", null, "loader:fastq load.py", "dst226_zbrf_clt___ACrdmct-age___48h_b03_t01_m01_R1.fastq.gz", "fastq", 2161847345.0, 35921817.0, "GSM7927518 r1", "0:60.18", "A:505467877;C:418329045;G:416403136;T:483063599;N:338583688", 60, null, null, null, 505467877, 418329045, 416403136, 483063599, 338583688, "SRX22707797", "SRS19700098", "SRA1761360", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.89532, null, 0.08355, null, 0.82012, null, 0.68413, null, 35, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2023-12-01", "Hatching", "Embryo", "Heart", "Cardiovascular System"], [29090, "SRR27015254", "SRX22707796", "SRS19700097", "SRP475323", "PRJNA1047551", "Identification of genes important during atrial myocardial morphogenesis", "GSE249149", "Transcriptome Analysis", "Atrial cardiomyocytes undergo complex cellular behaviours post 72 hpf to build muscle structures.  We aimed to identify the genes involved during this process  and therefore we seqeunced the RNA from 48 hpf and 72 hpf atrial cardiomyocytes to uncover changes in the transcirptome that might regulate or trigger atrial morphogenesis post 72 hpf. Overall design: Comparative gene expression profiling analysis of RNA seq data for 48 hpf and 72 hpf wild type zebrafish atrial cardiomyocytes.", null, "pubmed:39289341", null, "Wild type zebrafish atrial cardiomyocytes  48 hpf  rep 2", "GSM7927517", null, "source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocyte|genotype:wild type|treatment:48 hpf loc name:missing|collection date:missing", "Wild type zebrafish atrial cardiomyocytes  48 hpf  rep 2", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Dobin et al.  STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Assembly: danRer11 Supplementary files format and content: count matrix", "embryonic heart", null, "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "tissue:embryonic heart|cell type:cardiomyocyte|genotype:wild type|treatment:48 hpf", "GSM7927517", "GSM7927517: Wild type zebrafish atrial cardiomyocytes  48 hpf  rep 2; Danio rerio; RNA Seq", "GSM7927517 r1", "GSM7927517", "1", "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP475323", null, "loader:fastq load.py", "dst226_zbrf_clt___ACrdmct-age___48h_b02_t01_m01_R1.fastq.gz", "fastq", 2065547064.0, 31863833.0, "GSM7927517 r1", "0:64.82", "A:530497695;C:434164388;G:434118538;T:518043928;N:148722515", 64, null, null, null, 530497695, 434164388, 434118538, 518043928, 148722515, "SRX22707796", "SRS19700097", "SRA1761360", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.91772, null, 0.17863, null, 0.76828, null, 0.49567, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2023-12-01", "Hatching", "Embryo", "Heart", "Cardiovascular System"], [29091, "SRR27015255", "SRX22707795", "SRS19700096", "SRP475323", "PRJNA1047551", "Identification of genes important during atrial myocardial morphogenesis", "GSE249149", "Transcriptome Analysis", "Atrial cardiomyocytes undergo complex cellular behaviours post 72 hpf to build muscle structures.  We aimed to identify the genes involved during this process  and therefore we seqeunced the RNA from 48 hpf and 72 hpf atrial cardiomyocytes to uncover changes in the transcirptome that might regulate or trigger atrial morphogenesis post 72 hpf. Overall design: Comparative gene expression profiling analysis of RNA seq data for 48 hpf and 72 hpf wild type zebrafish atrial cardiomyocytes.", null, "pubmed:39289341", null, "Wild type zebrafish atrial cardiomyocytes  48 hpf  rep 1", "GSM7927516", null, "source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocyte|genotype:wild type|treatment:48 hpf loc name:missing|collection date:missing", "Wild type zebrafish atrial cardiomyocytes  48 hpf  rep 1", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Dobin et al.  STAR: ultrafast universal RNA seq aligner. Alignments were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Assembly: danRer11 Supplementary files format and content: count matrix", "embryonic heart", null, "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "tissue:embryonic heart|cell type:cardiomyocyte|genotype:wild type|treatment:48 hpf", "GSM7927516", "GSM7927516: Wild type zebrafish atrial cardiomyocytes  48 hpf  rep 1; Danio rerio; RNA Seq", "GSM7927516 r1", "GSM7927516", "1", "miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART\u00ae Seq HT Kit Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP475323", null, "loader:fastq load.py", "dst226_zbrf_clt___ACrdmct-age___48h_b01_t01_m01_R1.fastq.gz", "fastq", 1619268089.0, 24941754.0, "GSM7927516 r1", "0:64.92", "A:410578311;C:344485123;G:343852178;T:401558739;N:118793738", 64, null, null, null, 410578311, 344485123, 343852178, 401558739, 118793738, "SRX22707795", "SRS19700096", "SRA1761360", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.91693, null, 0.13175, null, 0.77082, null, 0.47511, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2023-12-01", "Hatching", "Embryo", "Heart", "Cardiovascular System"], [29145, "SRR32025076", "SRX27375413", "SRS23810876", "SRP476805", "PRJNA1050594", "Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture", "GSE249792", "Transcriptome Analysis", "Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.", null, null, null, "qKO 5  biol rep 1  adult aorta  3 aortas pooled", "GSM8741276", null, "source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:qKO|geo loc name:missing|collection date:missing", "qKO 5  biol rep 1  adult aorta  3 aortas pooled", "Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx", "pool of 3 adult aortas and bulbus arteriosus", null, "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3\u2019 mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", "Embryos were grown at 27\u00b0C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28\u00b0C  pH 7 5  conductivity 550\u00b5S and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.", "tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:qKO", "GSM8741276", "GSM8741276: qKO 5  biol rep 1  adult aorta  3 aortas pooled; Danio rerio; RNA Seq", "GSM8741276 r1", "GSM8741276", "1", "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ELEMENT", "Element AVITI", null, "SRP476805", null, null, "10_qKO_B9_R1.fastq.gz", "fastq", 1749103950.0, 23321386.0, "GSM8741276 r1", "0:75", "A:608737363;C:302455983;G:338119173;T:499492171;N:299260", 75, null, null, null, 608737363, 302455983, 338119173, 499492171, 299260, "SRX27375413", "SRS23810876", "SRA2053000", "Callewaert Lab, Biomolecular medicine, Ghent University", "Callewaert Lab, Biomolecular medicine, Ghent University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "element", "element", "3prime", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "Belgium", "2025-01-16", "Multi-stage", "Multi-stage", "Heart", "Cardiovascular System"], [29146, "SRR32025077", "SRX27375412", "SRS23810877", "SRP476805", "PRJNA1050594", "Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture", "GSE249792", "Transcriptome Analysis", "Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.", null, null, null, "qKO 4  biol rep 1  adult aorta  3 aortas pooled", "GSM8741275", null, "source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:qKO|geo loc name:missing|collection date:missing", "qKO 4  biol rep 1  adult aorta  3 aortas pooled", "Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx", "pool of 3 adult aortas and bulbus arteriosus", null, "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3\u2019 mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", "Embryos were grown at 27\u00b0C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28\u00b0C  pH 7 5  conductivity 550\u00b5S and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.", "tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:qKO", "GSM8741275", "GSM8741275: qKO 4  biol rep 1  adult aorta  3 aortas pooled; Danio rerio; RNA Seq", "GSM8741275 r1", "GSM8741275", "1", "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ELEMENT", "Element AVITI", null, "SRP476805", null, null, "9_qKO_A9_R1.fastq.gz", "fastq", 1391151150.0, 18548682.0, "GSM8741275 r1", "0:75", "A:493715157;C:235480005;G:265878909;T:395857913;N:219166", 75, null, null, null, 493715157, 235480005, 265878909, 395857913, 219166, "SRX27375412", "SRS23810877", "SRA2053000", "Callewaert Lab, Biomolecular medicine, Ghent University", "Callewaert Lab, Biomolecular medicine, Ghent University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "element", "element", "3prime", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "Belgium", "2025-01-16", "Multi-stage", "Multi-stage", "Heart", "Cardiovascular System"], [29147, "SRR32025078", "SRX27375411", "SRS23810875", "SRP476805", "PRJNA1050594", "Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture", "GSE249792", "Transcriptome Analysis", "Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.", null, null, null, "qKO 3  biol rep 1  adult aorta  3 aortas pooled", "GSM8741274", null, "source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:qKO|geo loc name:missing|collection date:missing", "qKO 3  biol rep 1  adult aorta  3 aortas pooled", "Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx", "pool of 3 adult aortas and bulbus arteriosus", null, "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3\u2019 mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", "Embryos were grown at 27\u00b0C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28\u00b0C  pH 7 5  conductivity 550\u00b5S and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.", "tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:qKO", "GSM8741274", "GSM8741274: qKO 3  biol rep 1  adult aorta  3 aortas pooled; Danio rerio; RNA Seq", "GSM8741274 r1", "GSM8741274", "1", "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ELEMENT", "Element AVITI", null, "SRP476805", null, null, "8_qKO_H8_R1.fastq.gz", "fastq", 1548693000.0, 20649240.0, "GSM8741274 r1", "0:75", "A:546086416;C:265907989;G:302995102;T:433434795;N:268698", 75, null, null, null, 546086416, 265907989, 302995102, 433434795, 268698, "SRX27375411", "SRS23810875", "SRA2053000", "Callewaert Lab, Biomolecular medicine, Ghent University", "Callewaert Lab, Biomolecular medicine, Ghent University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "element", "element", "3prime", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "Belgium", "2025-01-16", "Multi-stage", "Multi-stage", "Heart", "Cardiovascular System"], [29148, "SRR32025079", "SRX27375410", "SRS23810873", "SRP476805", "PRJNA1050594", "Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture", "GSE249792", "Transcriptome Analysis", "Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.", null, null, null, "qKO 2  biol rep 1  adult aorta  3 aortas pooled", "GSM8741273", null, "source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:qKO|geo loc name:missing|collection date:missing", "qKO 2  biol rep 1  adult aorta  3 aortas pooled", "Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx", "pool of 3 adult aortas and bulbus arteriosus", null, "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3\u2019 mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", "Embryos were grown at 27\u00b0C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28\u00b0C  pH 7 5  conductivity 550\u00b5S and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.", "tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:qKO", "GSM8741273", "GSM8741273: qKO 2  biol rep 1  adult aorta  3 aortas pooled; Danio rerio; RNA Seq", "GSM8741273 r1", "GSM8741273", "1", "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ELEMENT", "Element AVITI", null, "SRP476805", null, null, "7_qKO_G8_R1.fastq.gz", "fastq", 1420837575.0, 18944501.0, "GSM8741273 r1", "0:75", "A:505066296;C:237130175;G:277345211;T:401058536;N:237357", 75, null, null, null, 505066296, 237130175, 277345211, 401058536, 237357, "SRX27375410", "SRS23810873", "SRA2053000", "Callewaert Lab, Biomolecular medicine, Ghent University", "Callewaert Lab, Biomolecular medicine, Ghent University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "element", "element", "3prime", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "Belgium", "2025-01-16", "Multi-stage", "Multi-stage", "Heart", "Cardiovascular System"], [29149, "SRR32025080", "SRX27375409", "SRS23810874", "SRP476805", "PRJNA1050594", "Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture", "GSE249792", "Transcriptome Analysis", "Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.", null, null, null, "qKO 1  biol rep 1  adult aorta  3 aortas pooled", "GSM8741272", null, "source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:qKO|geo loc name:missing|collection date:missing", "qKO 1  biol rep 1  adult aorta  3 aortas pooled", "Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx", "pool of 3 adult aortas and bulbus arteriosus", null, "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3\u2019 mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", "Embryos were grown at 27\u00b0C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28\u00b0C  pH 7 5  conductivity 550\u00b5S and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.", "tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:qKO", "GSM8741272", "GSM8741272: qKO 1  biol rep 1  adult aorta  3 aortas pooled; Danio rerio; RNA Seq", "GSM8741272 r1", "GSM8741272", "1", "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ELEMENT", "Element AVITI", null, "SRP476805", null, null, "6_qKO_F8_R1.fastq.gz", "fastq", 1486031025.0, 19813747.0, "GSM8741272 r1", "0:75", "A:520876345;C:250796628;G:293184034;T:420907913;N:266105", 75, null, null, null, 520876345, 250796628, 293184034, 420907913, 266105, "SRX27375409", "SRS23810874", "SRA2053000", "Callewaert Lab, Biomolecular medicine, Ghent University", "Callewaert Lab, Biomolecular medicine, Ghent University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "element", "element", "3prime", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "Belgium", "2025-01-16", "Multi-stage", "Multi-stage", "Heart", "Cardiovascular System"], [29150, "SRR32025081", "SRX27375408", "SRS23810872", "SRP476805", "PRJNA1050594", "Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture", "GSE249792", "Transcriptome Analysis", "Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.", null, null, null, "control 5  biol rep 1  adult aorta  3 aortas pooled", "GSM8741271", null, "source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:wt control|geo loc name:missing|collection date:missing", "control 5  biol rep 1  adult aorta  3 aortas pooled", "Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx", "pool of 3 adult aortas and bulbus arteriosus", null, "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3\u2019 mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", "Embryos were grown at 27\u00b0C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28\u00b0C  pH 7 5  conductivity 550\u00b5S and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.", "tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:wt control", "GSM8741271", "GSM8741271: control 5  biol rep 1  adult aorta  3 aortas pooled; Danio rerio; RNA Seq", "GSM8741271 r1", "GSM8741271", "1", "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ELEMENT", "Element AVITI", null, "SRP476805", null, null, "5_wt_control_E8_R1.fastq.gz", "fastq", 1415975175.0, 18879669.0, "GSM8741271 r1", "0:75", "A:499498659;C:237283969;G:278581269;T:400389063;N:222215", 75, null, null, null, 499498659, 237283969, 278581269, 400389063, 222215, "SRX27375408", "SRS23810872", "SRA2053000", "Callewaert Lab, Biomolecular medicine, Ghent University", "Callewaert Lab, Biomolecular medicine, Ghent University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "element", "element", "3prime", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "Belgium", "2025-01-16", "Multi-stage", "Multi-stage", "Heart", "Cardiovascular System"], [29151, "SRR32025082", "SRX27375407", "SRS23810871", "SRP476805", "PRJNA1050594", "Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture", "GSE249792", "Transcriptome Analysis", "Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.", null, null, null, "control 4  biol rep 1  adult aorta  3 aortas pooled", "GSM8741270", null, "source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:wt control|geo loc name:missing|collection date:missing", "control 4  biol rep 1  adult aorta  3 aortas pooled", "Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx", "pool of 3 adult aortas and bulbus arteriosus", null, "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3\u2019 mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", "Embryos were grown at 27\u00b0C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28\u00b0C  pH 7 5  conductivity 550\u00b5S and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.", "tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:wt control", "GSM8741270", "GSM8741270: control 4  biol rep 1  adult aorta  3 aortas pooled; Danio rerio; RNA Seq", "GSM8741270 r1", "GSM8741270", "1", "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ELEMENT", "Element AVITI", null, "SRP476805", null, null, "4_wt_control_D8_R1.fastq.gz", "fastq", 1448565375.0, 19314205.0, "GSM8741270 r1", "0:75", "A:515361139;C:240035739;G:286658162;T:406262131;N:248204", 75, null, null, null, 515361139, 240035739, 286658162, 406262131, 248204, "SRX27375407", "SRS23810871", "SRA2053000", "Callewaert Lab, Biomolecular medicine, Ghent University", "Callewaert Lab, Biomolecular medicine, Ghent University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "element", "element", "3prime", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "Belgium", "2025-01-16", "Multi-stage", "Multi-stage", "Heart", "Cardiovascular System"], [29152, "SRR32025083", "SRX27375406", "SRS23810870", "SRP476805", "PRJNA1050594", "Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture", "GSE249792", "Transcriptome Analysis", "Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.", null, null, null, "control 3  biol rep 1  adult aorta  3 aortas pooled", "GSM8741269", null, "source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:wt control|geo loc name:missing|collection date:missing", "control 3  biol rep 1  adult aorta  3 aortas pooled", "Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx", "pool of 3 adult aortas and bulbus arteriosus", null, "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3\u2019 mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", "Embryos were grown at 27\u00b0C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28\u00b0C  pH 7 5  conductivity 550\u00b5S and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.", "tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:wt control", "GSM8741269", "GSM8741269: control 3  biol rep 1  adult aorta  3 aortas pooled; Danio rerio; RNA Seq", "GSM8741269 r1", "GSM8741269", "1", "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ELEMENT", "Element AVITI", null, "SRP476805", null, null, "3_wt_control_C8_R1.fastq.gz", "fastq", 1171513275.0, 15620177.0, "GSM8741269 r1", "0:75", "A:417371801;C:198042286;G:227929434;T:328006138;N:163616", 75, null, null, null, 417371801, 198042286, 227929434, 328006138, 163616, "SRX27375406", "SRS23810870", "SRA2053000", "Callewaert Lab, Biomolecular medicine, Ghent University", "Callewaert Lab, Biomolecular medicine, Ghent University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "element", "element", "3prime", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "Belgium", "2025-01-16", "Multi-stage", "Multi-stage", "Heart", "Cardiovascular System"], [29153, "SRR32025084", "SRX27375405", "SRS23810869", "SRP476805", "PRJNA1050594", "Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture", "GSE249792", "Transcriptome Analysis", "Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.", null, null, null, "control 2  biol rep 1  adult aorta  3 aortas pooled", "GSM8741268", null, "source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:wt control|geo loc name:missing|collection date:missing", "control 2  biol rep 1  adult aorta  3 aortas pooled", "Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx", "pool of 3 adult aortas and bulbus arteriosus", null, "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3\u2019 mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", "Embryos were grown at 27\u00b0C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28\u00b0C  pH 7 5  conductivity 550\u00b5S and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.", "tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:wt control", "GSM8741268", "GSM8741268: control 2  biol rep 1  adult aorta  3 aortas pooled; Danio rerio; RNA Seq", "GSM8741268 r1", "GSM8741268", "1", "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ELEMENT", "Element AVITI", null, "SRP476805", null, null, "2_wt_control_B8_R1.fastq.gz", "fastq", 1379973000.0, 18399640.0, "GSM8741268 r1", "0:75", "A:487735196;C:232122567;G:270442978;T:389464154;N:208105", 75, null, null, null, 487735196, 232122567, 270442978, 389464154, 208105, "SRX27375405", "SRS23810869", "SRA2053000", "Callewaert Lab, Biomolecular medicine, Ghent University", "Callewaert Lab, Biomolecular medicine, Ghent University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "element", "element", "3prime", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "Belgium", "2025-01-16", "Multi-stage", "Multi-stage", "Heart", "Cardiovascular System"], [29154, "SRR32025085", "SRX27375404", "SRS23810868", "SRP476805", "PRJNA1050594", "Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture", "GSE249792", "Transcriptome Analysis", "Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.", null, null, null, "control 1  biol rep 1  adult aorta  3 aortas pooled", "GSM8741267", null, "source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:wt control|geo loc name:missing|collection date:missing", "control 1  biol rep 1  adult aorta  3 aortas pooled", "Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx", "pool of 3 adult aortas and bulbus arteriosus", null, "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3\u2019 mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", "Embryos were grown at 27\u00b0C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28\u00b0C  pH 7 5  conductivity 550\u00b5S and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.", "tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:wt control", "GSM8741267", "GSM8741267: control 1  biol rep 1  adult aorta  3 aortas pooled; Danio rerio; RNA Seq", "GSM8741267 r1", "GSM8741267", "1", "For RNA extraction  the Rneasy\u00ae minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ELEMENT", "Element AVITI", null, "SRP476805", null, null, "1_wt_control_A8_R1.fastq.gz", "fastq", 1068193125.0, 14242575.0, "GSM8741267 r1", "0:75", "A:379776425;C:179521683;G:209337737;T:299415096;N:142184", 75, null, null, null, 379776425, 179521683, 209337737, 299415096, 142184, "SRX27375404", "SRS23810868", "SRA2053000", "Callewaert Lab, Biomolecular medicine, Ghent University", "Callewaert Lab, Biomolecular medicine, Ghent University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "element", "element", "3prime", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "Belgium", "2025-01-16", "Multi-stage", "Multi-stage", "Heart", "Cardiovascular System"], [29569, "SRR27368685", "SRX23045203", "SRS20006222", "SRP480346", "PRJNA1057908", "An in vivo repertoire of zebrafish cardiomyocyte specific cis regulatory elements [RNA Seq]", "GSE252151", "Transcriptome Analysis", "cis Regulatory elements cREs are essential for the spatio temporal control of gene expression during development and disease. However  cRE activity is highly dependent on cell and tissue type. The developing heart is composed of several cell types  predominantly cardiomyocytes. Therefore  cardiomyocytes specific modelling is required to understand the cis regulation of the developing heart. Zebrafish are an ideal model to study heart development  as they share a number of physiological features with the human heart during development. Therefore  we present a comprehensive cardiomyocyte specific repertoire of cREs isolated from zebrafish larvae. This data combines live transcriptomics and epigenetic profiling  providing insights into cREs and their associated genes involved in heart development. We further perform a transgenic reporter assay for the identified cREs of bmp10 and popdc2 genes  validating these genomic regions as cardiac regulatory elements. We share this comprehensive  reproducible cardiomyocyte specific cRE resource as an interrogable web tool for understanding the epigenetic and transcriptomic mechanisms underlying heart development and emergence of congenital heart defects. Overall design: Cardiomyocytes were isolated from the Tgmyl7::GFP zebrafish transgenic line. Larvae were collected 72 hpf GFP positive 30 000 cells  n=3 biological replicates and GFP negative cells 500 000 cells  n=3 biological replicates were collected  and RNA sequencing was performed on these samples.", "parent bioproject:PRJNA1057890", null, null, "500kGFPneg6 Non cardiomyocytes", "GSM7995233", null, "source name:Heart|tissue:Heart|cell line:Primary cells|cell type:Non cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPneg|treatment:Control|geo loc name:missing|collection date:missing", "500kGFPneg6 Non cardiomyocytes", "FASTQ files were quality trimmed for overrepresented sequences using Cutadapt version 1.16 Martin  2011. The files were then processed for mapping and obtaining read counts with RNAsik Tsyganov et al  2018  using default parameters. There were two sets of counts obtained  the first were the reads mapped to genome Zv9  and the second to genome Zv10. Read counts obtained from mapping to Zv10 were used for RNA seq analysis and visualizations. Read counts obtained from mapping to Zv9 were used for RNA seq analysis to obtain a set of DEGs and were then used to overlap with the genes associated to peaks of the ChIP seq data sets. Assembly: Zv9  Zv10 Supplementary files format and content: txt.gz: compressed tab delimited text files include count values for each sample", "Heart", null, "RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866  Qubit\u2122 RNA HS Assay Kit Q32852  ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Heart|cell line:Primary cells|cell type:Non cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPneg|treatment:Control", "GSM7995233", "GSM7995233: 500kGFPneg6 Non cardiomyocytes; Danio rerio; RNA Seq", "GSM7995233 r1", "GSM7995233", "1", "RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866  Qubit\u2122 RNA HS Assay Kit Q32852  ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP480346", null, null, "500kGFPneg6_S42_L008_R1_001.fastq.gz", "fastq", 527477356.0, 10449387.0, "GSM7995233 r1", "0:50.48", "A:141759410;C:113279303;G:116384028;T:155860577;N:194038", 50, null, null, null, 141759410, 113279303, 116384028, 155860577, 194038, "SRX23045203", "SRS20006222", "SRA1776396", "Australian Regenerative Medicine Institute, Monash University", "Australian Regenerative Medicine Institute, Monash University", 1, 0.79175, null, 0.2711, null, 0.7587, null, 0.61924, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-12-27", "Undetermined", "Larval", "Heart", "Cardiovascular System"], [29570, "SRR27368686", "SRX23045202", "SRS20006221", "SRP480346", "PRJNA1057908", "An in vivo repertoire of zebrafish cardiomyocyte specific cis regulatory elements [RNA Seq]", "GSE252151", "Transcriptome Analysis", "cis Regulatory elements cREs are essential for the spatio temporal control of gene expression during development and disease. However  cRE activity is highly dependent on cell and tissue type. The developing heart is composed of several cell types  predominantly cardiomyocytes. Therefore  cardiomyocytes specific modelling is required to understand the cis regulation of the developing heart. Zebrafish are an ideal model to study heart development  as they share a number of physiological features with the human heart during development. Therefore  we present a comprehensive cardiomyocyte specific repertoire of cREs isolated from zebrafish larvae. This data combines live transcriptomics and epigenetic profiling  providing insights into cREs and their associated genes involved in heart development. We further perform a transgenic reporter assay for the identified cREs of bmp10 and popdc2 genes  validating these genomic regions as cardiac regulatory elements. We share this comprehensive  reproducible cardiomyocyte specific cRE resource as an interrogable web tool for understanding the epigenetic and transcriptomic mechanisms underlying heart development and emergence of congenital heart defects. Overall design: Cardiomyocytes were isolated from the Tgmyl7::GFP zebrafish transgenic line. Larvae were collected 72 hpf GFP positive 30 000 cells  n=3 biological replicates and GFP negative cells 500 000 cells  n=3 biological replicates were collected  and RNA sequencing was performed on these samples.", "parent bioproject:PRJNA1057890", null, null, "500kGFPneg5 Non cardiomyocytes", "GSM7995232", null, "source name:Heart|tissue:Heart|cell line:Primary cells|cell type:Non cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPneg|treatment:Control|geo loc name:missing|collection date:missing", "500kGFPneg5 Non cardiomyocytes", "FASTQ files were quality trimmed for overrepresented sequences using Cutadapt version 1.16 Martin  2011. The files were then processed for mapping and obtaining read counts with RNAsik Tsyganov et al  2018  using default parameters. There were two sets of counts obtained  the first were the reads mapped to genome Zv9  and the second to genome Zv10. Read counts obtained from mapping to Zv10 were used for RNA seq analysis and visualizations. Read counts obtained from mapping to Zv9 were used for RNA seq analysis to obtain a set of DEGs and were then used to overlap with the genes associated to peaks of the ChIP seq data sets. Assembly: Zv9  Zv10 Supplementary files format and content: txt.gz: compressed tab delimited text files include count values for each sample", "Heart", null, "RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866  Qubit\u2122 RNA HS Assay Kit Q32852  ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Heart|cell line:Primary cells|cell type:Non cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPneg|treatment:Control", "GSM7995232", "GSM7995232: 500kGFPneg5 Non cardiomyocytes; Danio rerio; RNA Seq", "GSM7995232 r1", "GSM7995232", "1", "RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866  Qubit\u2122 RNA HS Assay Kit Q32852  ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP480346", null, null, "500kGFPneg5_S41_L008_R1_001.fastq.gz", "fastq", 3356204764.0, 66511806.0, "GSM7995232 r1", "0:50.46", "A:860342578;C:766593257;G:774473426;T:953992775;N:802728", 50, null, null, null, 860342578, 766593257, 774473426, 953992775, 802728, "SRX23045202", "SRS20006221", "SRA1776396", "Australian Regenerative Medicine Institute, Monash University", "Australian Regenerative Medicine Institute, Monash University", 1, 0.70469, null, 0.23332, null, 0.76992, null, 0.62712, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-12-27", "Undetermined", "Larval", "Heart", "Cardiovascular System"], [29571, "SRR27368687", "SRX23045201", "SRS20006220", "SRP480346", "PRJNA1057908", "An in vivo repertoire of zebrafish cardiomyocyte specific cis regulatory elements [RNA Seq]", "GSE252151", "Transcriptome Analysis", "cis Regulatory elements cREs are essential for the spatio temporal control of gene expression during development and disease. However  cRE activity is highly dependent on cell and tissue type. The developing heart is composed of several cell types  predominantly cardiomyocytes. Therefore  cardiomyocytes specific modelling is required to understand the cis regulation of the developing heart. Zebrafish are an ideal model to study heart development  as they share a number of physiological features with the human heart during development. Therefore  we present a comprehensive cardiomyocyte specific repertoire of cREs isolated from zebrafish larvae. This data combines live transcriptomics and epigenetic profiling  providing insights into cREs and their associated genes involved in heart development. We further perform a transgenic reporter assay for the identified cREs of bmp10 and popdc2 genes  validating these genomic regions as cardiac regulatory elements. We share this comprehensive  reproducible cardiomyocyte specific cRE resource as an interrogable web tool for understanding the epigenetic and transcriptomic mechanisms underlying heart development and emergence of congenital heart defects. Overall design: Cardiomyocytes were isolated from the Tgmyl7::GFP zebrafish transgenic line. Larvae were collected 72 hpf GFP positive 30 000 cells  n=3 biological replicates and GFP negative cells 500 000 cells  n=3 biological replicates were collected  and RNA sequencing was performed on these samples.", "parent bioproject:PRJNA1057890", null, null, "500kGFPneg4 Non cardiomyocytes", "GSM7995231", null, "source name:Heart|tissue:Heart|cell line:Primary cells|cell type:Non cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPneg|treatment:Control|geo loc name:missing|collection date:missing", "500kGFPneg4 Non cardiomyocytes", "FASTQ files were quality trimmed for overrepresented sequences using Cutadapt version 1.16 Martin  2011. The files were then processed for mapping and obtaining read counts with RNAsik Tsyganov et al  2018  using default parameters. There were two sets of counts obtained  the first were the reads mapped to genome Zv9  and the second to genome Zv10. Read counts obtained from mapping to Zv10 were used for RNA seq analysis and visualizations. Read counts obtained from mapping to Zv9 were used for RNA seq analysis to obtain a set of DEGs and were then used to overlap with the genes associated to peaks of the ChIP seq data sets. Assembly: Zv9  Zv10 Supplementary files format and content: txt.gz: compressed tab delimited text files include count values for each sample", "Heart", null, "RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866  Qubit\u2122 RNA HS Assay Kit Q32852  ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Heart|cell line:Primary cells|cell type:Non cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPneg|treatment:Control", "GSM7995231", "GSM7995231: 500kGFPneg4 Non cardiomyocytes; Danio rerio; RNA Seq", "GSM7995231 r1", "GSM7995231", "1", "RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866  Qubit\u2122 RNA HS Assay Kit Q32852  ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP480346", null, null, "500kGFPneg4_S40_L008_R1_001.fastq.gz", "fastq", 3075367681.0, 60986692.0, "GSM7995231 r1", "0:50.43", "A:807059039;C:682279458;G:696326840;T:888937765;N:764579", 50, null, null, null, 807059039, 682279458, 696326840, 888937765, 764579, "SRX23045201", "SRS20006220", "SRA1776396", "Australian Regenerative Medicine Institute, Monash University", "Australian Regenerative Medicine Institute, Monash University", 1, 0.74255, null, 0.26699, null, 0.76786, null, 0.63053, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-12-27", "Undetermined", "Larval", "Heart", "Cardiovascular System"], [29572, "SRR27368688", "SRX23045200", "SRS20006219", "SRP480346", "PRJNA1057908", "An in vivo repertoire of zebrafish cardiomyocyte specific cis regulatory elements [RNA Seq]", "GSE252151", "Transcriptome Analysis", "cis Regulatory elements cREs are essential for the spatio temporal control of gene expression during development and disease. However  cRE activity is highly dependent on cell and tissue type. The developing heart is composed of several cell types  predominantly cardiomyocytes. Therefore  cardiomyocytes specific modelling is required to understand the cis regulation of the developing heart. Zebrafish are an ideal model to study heart development  as they share a number of physiological features with the human heart during development. Therefore  we present a comprehensive cardiomyocyte specific repertoire of cREs isolated from zebrafish larvae. This data combines live transcriptomics and epigenetic profiling  providing insights into cREs and their associated genes involved in heart development. We further perform a transgenic reporter assay for the identified cREs of bmp10 and popdc2 genes  validating these genomic regions as cardiac regulatory elements. We share this comprehensive  reproducible cardiomyocyte specific cRE resource as an interrogable web tool for understanding the epigenetic and transcriptomic mechanisms underlying heart development and emergence of congenital heart defects. Overall design: Cardiomyocytes were isolated from the Tgmyl7::GFP zebrafish transgenic line. Larvae were collected 72 hpf GFP positive 30 000 cells  n=3 biological replicates and GFP negative cells 500 000 cells  n=3 biological replicates were collected  and RNA sequencing was performed on these samples.", "parent bioproject:PRJNA1057890", null, null, "30kGFPpos3 Cardiomyocytes", "GSM7995230", null, "source name:Heart|tissue:Heart|cell line:Primary cells|cell type:Cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPpos|treatment:Control|geo loc name:missing|collection date:missing", "30kGFPpos3 Cardiomyocytes", "FASTQ files were quality trimmed for overrepresented sequences using Cutadapt version 1.16 Martin  2011. The files were then processed for mapping and obtaining read counts with RNAsik Tsyganov et al  2018  using default parameters. There were two sets of counts obtained  the first were the reads mapped to genome Zv9  and the second to genome Zv10. Read counts obtained from mapping to Zv10 were used for RNA seq analysis and visualizations. Read counts obtained from mapping to Zv9 were used for RNA seq analysis to obtain a set of DEGs and were then used to overlap with the genes associated to peaks of the ChIP seq data sets. Assembly: Zv9  Zv10 Supplementary files format and content: txt.gz: compressed tab delimited text files include count values for each sample", "Heart", null, "RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866  Qubit\u2122 RNA HS Assay Kit Q32852  ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Heart|cell line:Primary cells|cell type:Cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPpos|treatment:Control", "GSM7995230", "GSM7995230: 30kGFPpos3 Cardiomyocytes; Danio rerio; RNA Seq", "GSM7995230 r1", "GSM7995230", "1", "RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866  Qubit\u2122 RNA HS Assay Kit Q32852  ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP480346", null, null, "30kGFPpos3_S39_L008_R1_001.fastq.gz", "fastq", 2938808771.0, 58361915.0, "GSM7995230 r1", "0:50.35", "A:533261626;C:883704329;G:825929620;T:694986734;N:926462", 50, null, null, null, 533261626, 883704329, 825929620, 694986734, 926462, "SRX23045200", "SRS20006219", "SRA1776396", "Australian Regenerative Medicine Institute, Monash University", "Australian Regenerative Medicine Institute, Monash University", 1, 0.12924, null, 0.05415, null, 0.92034, null, 0.70896, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-12-27", "Undetermined", "Larval", "Heart", "Cardiovascular System"], [29573, "SRR27368689", "SRX23045199", "SRS20006218", "SRP480346", "PRJNA1057908", "An in vivo repertoire of zebrafish cardiomyocyte specific cis regulatory elements [RNA Seq]", "GSE252151", "Transcriptome Analysis", "cis Regulatory elements cREs are essential for the spatio temporal control of gene expression during development and disease. However  cRE activity is highly dependent on cell and tissue type. The developing heart is composed of several cell types  predominantly cardiomyocytes. Therefore  cardiomyocytes specific modelling is required to understand the cis regulation of the developing heart. Zebrafish are an ideal model to study heart development  as they share a number of physiological features with the human heart during development. Therefore  we present a comprehensive cardiomyocyte specific repertoire of cREs isolated from zebrafish larvae. This data combines live transcriptomics and epigenetic profiling  providing insights into cREs and their associated genes involved in heart development. We further perform a transgenic reporter assay for the identified cREs of bmp10 and popdc2 genes  validating these genomic regions as cardiac regulatory elements. We share this comprehensive  reproducible cardiomyocyte specific cRE resource as an interrogable web tool for understanding the epigenetic and transcriptomic mechanisms underlying heart development and emergence of congenital heart defects. Overall design: Cardiomyocytes were isolated from the Tgmyl7::GFP zebrafish transgenic line. Larvae were collected 72 hpf GFP positive 30 000 cells  n=3 biological replicates and GFP negative cells 500 000 cells  n=3 biological replicates were collected  and RNA sequencing was performed on these samples.", "parent bioproject:PRJNA1057890", null, null, "30kGFPpos2 Cardiomyocytes", "GSM7995229", null, "source name:Heart|tissue:Heart|cell line:Primary cells|cell type:Cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPpos|treatment:Control|geo loc name:missing|collection date:missing", "30kGFPpos2 Cardiomyocytes", "FASTQ files were quality trimmed for overrepresented sequences using Cutadapt version 1.16 Martin  2011. The files were then processed for mapping and obtaining read counts with RNAsik Tsyganov et al  2018  using default parameters. There were two sets of counts obtained  the first were the reads mapped to genome Zv9  and the second to genome Zv10. Read counts obtained from mapping to Zv10 were used for RNA seq analysis and visualizations. Read counts obtained from mapping to Zv9 were used for RNA seq analysis to obtain a set of DEGs and were then used to overlap with the genes associated to peaks of the ChIP seq data sets. Assembly: Zv9  Zv10 Supplementary files format and content: txt.gz: compressed tab delimited text files include count values for each sample", "Heart", null, "RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866  Qubit\u2122 RNA HS Assay Kit Q32852  ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Heart|cell line:Primary cells|cell type:Cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPpos|treatment:Control", "GSM7995229", "GSM7995229: 30kGFPpos2 Cardiomyocytes; Danio rerio; RNA Seq", "GSM7995229 r1", "GSM7995229", "1", "RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866  Qubit\u2122 RNA HS Assay Kit Q32852  ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP480346", null, null, "30kGFPpos2_S38_L008_R1_001.fastq.gz", "fastq", 3006409096.0, 59645543.0, "GSM7995229 r1", "0:50.40", "A:560839480;C:885691877;G:830121593;T:728932219;N:823927", 50, null, null, null, 560839480, 885691877, 830121593, 728932219, 823927, "SRX23045199", "SRS20006218", "SRA1776396", "Australian Regenerative Medicine Institute, Monash University", "Australian Regenerative Medicine Institute, Monash University", 1, 0.17805, null, 0.06115, null, 0.89769, null, 0.68731, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-12-27", "Undetermined", "Larval", "Heart", "Cardiovascular System"], [29574, "SRR27368690", "SRX23045198", "SRS20006217", "SRP480346", "PRJNA1057908", "An in vivo repertoire of zebrafish cardiomyocyte specific cis regulatory elements [RNA Seq]", "GSE252151", "Transcriptome Analysis", "cis Regulatory elements cREs are essential for the spatio temporal control of gene expression during development and disease. However  cRE activity is highly dependent on cell and tissue type. The developing heart is composed of several cell types  predominantly cardiomyocytes. Therefore  cardiomyocytes specific modelling is required to understand the cis regulation of the developing heart. Zebrafish are an ideal model to study heart development  as they share a number of physiological features with the human heart during development. Therefore  we present a comprehensive cardiomyocyte specific repertoire of cREs isolated from zebrafish larvae. This data combines live transcriptomics and epigenetic profiling  providing insights into cREs and their associated genes involved in heart development. We further perform a transgenic reporter assay for the identified cREs of bmp10 and popdc2 genes  validating these genomic regions as cardiac regulatory elements. We share this comprehensive  reproducible cardiomyocyte specific cRE resource as an interrogable web tool for understanding the epigenetic and transcriptomic mechanisms underlying heart development and emergence of congenital heart defects. Overall design: Cardiomyocytes were isolated from the Tgmyl7::GFP zebrafish transgenic line. Larvae were collected 72 hpf GFP positive 30 000 cells  n=3 biological replicates and GFP negative cells 500 000 cells  n=3 biological replicates were collected  and RNA sequencing was performed on these samples.", "parent bioproject:PRJNA1057890", null, null, "30kGFPpos1 Cardiomyocytes", "GSM7995228", null, "source name:Heart|tissue:Heart|cell line:Primary cells|cell type:Cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPpos|treatment:Control|geo loc name:missing|collection date:missing", "30kGFPpos1 Cardiomyocytes", "FASTQ files were quality trimmed for overrepresented sequences using Cutadapt version 1.16 Martin  2011. The files were then processed for mapping and obtaining read counts with RNAsik Tsyganov et al  2018  using default parameters. There were two sets of counts obtained  the first were the reads mapped to genome Zv9  and the second to genome Zv10. Read counts obtained from mapping to Zv10 were used for RNA seq analysis and visualizations. Read counts obtained from mapping to Zv9 were used for RNA seq analysis to obtain a set of DEGs and were then used to overlap with the genes associated to peaks of the ChIP seq data sets. Assembly: Zv9  Zv10 Supplementary files format and content: txt.gz: compressed tab delimited text files include count values for each sample", "Heart", null, "RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866  Qubit\u2122 RNA HS Assay Kit Q32852  ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Heart|cell line:Primary cells|cell type:Cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPpos|treatment:Control", "GSM7995228", "GSM7995228: 30kGFPpos1 Cardiomyocytes; Danio rerio; RNA Seq", "GSM7995228 r1", "GSM7995228", "1", "RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866  Qubit\u2122 RNA HS Assay Kit Q32852  ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP480346", null, null, "30kGFPpos1_S37_L008_R1_001.fastq.gz", "fastq", 3254639839.0, 64665631.0, "GSM7995228 r1", "0:50.33", "A:545193535;C:1023804678;G:938318027;T:746302007;N:1021592", 50, null, null, null, 545193535, 1023804678, 938318027, 746302007, 1021592, "SRX23045198", "SRS20006217", "SRA1776396", "Australian Regenerative Medicine Institute, Monash University", "Australian Regenerative Medicine Institute, Monash University", 1, 0.05453, null, 0.01921, null, 0.9643, null, 0.78064, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-12-27", "Undetermined", "Larval", "Heart", "Cardiovascular System"], [30006, "SRR27663958", "SRX23331822", "SRS20194274", "SRP484810", "PRJNA1066877", "p65 signaling dynamics drive the developmental progression of hematopoietic stem and progenitor cells through cell cycle regulation", "GSE253758", "Transcriptome Analysis", "While hematopoietic stem and progenitor cells HSPCs and the signaling pathways that specify them have been well defined in vivo  deriving functional HSPCs from human pluripotent stem cells hPSCs is still an outstanding challenge in the stem cell field. This has impaired efforts to use patient specific HSPCs and their derivatives to treat leukemia  lymphoma  anemia  and solid cancers. Identifying the missing element to derive functional human HSPCs will be critical to advance these therapies. Here  we found that in contrast to in vitro protocols where signaling pathways are typically manipulated statically  the natural developmental progression of HSPC fate in the embryo requires a precise and temporally controlled oscillatory signaling dynamics.  Particularly  our work reveals that NF kB signaling works as an oscillatory clock that controls the developmental progression of HSPCs by driving phases of quiescence and proliferation precisely during embryonic development. This was revealed by live imaging of a custom NF kB zebrafish reporter line  in conjunction with transcriptomic profiling and precise temporal manipulations of the NF kB family member p65  the driver of these signaling events. We also show that in vitro protocols of human hematopoietic differentiation from iPSCs depend on initial pro inflammatory signaling activation. In summary  our results uncover the functional role of pro inflammatory signaling during HSPC specification  revealed their oscillatory dynamics  and define this signaling pathway as the main driver of HSPC fate progression. The integration of these dynamics in vitro will be fundamental to achieve the long standing goal of generating and expanding patient derived functional HSPCs. Overall design: To gain insights into how NF kB in endothelium was contributing to HSPC specification  NFKB+ or NFKB  endothelial cells kdrl+ were sorted and collected from 22hpf zebrafish embryos in triplicate and subject to RNA seq.", null, "pubmed:39242546", null, "NFKB   biol rep 3", "GSM8027552", null, "tissue:endothelial cells|cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB  sorted|geo loc name:missing|collection date:missing", "NFKB   biol rep 3", "Data was analyzed by ROSALIND\u00ae https://rosalind.bio/  with a HyperScale architecture developed by ROSALIND  Inc. San Diego  CA. Reads were trimmed using cutadapt. Reads were aligned to the Danio rerio genome build danRer10 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression RLE using DESeq2. Assembly: danRer10 Supplementary files format and content: comma delimited text files include fold change  p values  adjusted p values  and normalized abundance values per sample for each gene", "endothelial cells", "22hpf NFKB:d2eGFP x kdrl:mCherry zebrafish embryos were screened with Leica M165FC stereomicroscope  dechorionated with pronase Millipore Sigma; 11459643001  anesthetized in 1% tricaine Pentair; TRS5 and dissociated. Specifically  the trunk region of each embryo was surgically isolated posterior to the yolk ball and anterior to the urogenital canal using a scalpel. The collected tissue was then gently vortexed at 28C for 5 20 mins with 50 \u00b5g/ml Liberase TM Millipore Sigma: 5401127001 in Dulbecco\u2032s Phosphate Buffered Saline solution with Ca2+ and Mg2+ Millipore Sigma  D8662. The resulting cell suspension was filtered through 30 \u00b5m nylon mesh Fisher Scientific; NC9084441 using a 21 gauge syringe Fisher Scientific; BD 309624 and stained with SYTOX\u2122 Red Life Technologies; S34859 to exclude dead cells. Kdrl+/NFKB  and kdrl+/NFKB+ cells were each sorted and collected with BD FACS Aria III. 7 000 cells per sample were collected by FACS in Eppendorf tubes containing 250 \u00b5l of RLT buffer.", "RNA was then isolated and purified with RNeasy\u00ae Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer\u2019s instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.", "Zebrafish Danio rerio embryos and adults were mated  staged  raised  and processed in a circulating aquarium system maintained at 26 \u00b0C on a 14 hr light/10 hr dark cycle.", "cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB  sorted", "GSM8027552", "GSM8027552: NFKB   biol rep 3; Danio rerio; RNA Seq", "GSM8027552 r1", "GSM8027552", "1", "RNA was then isolated and purified with RNeasy\u00ae Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer's instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484810", null, "loader:fastq load.py", "6-RNA-1001_S6_L001_R1_001.fastq.gz", "fastq", 7566894200.0, 75668942.0, "GSM8027552 r1", "0:100", "A:2055514007;C:1776454819;G:1779667416;T:1955100553;N:157405", 100, null, null, null, 2055514007, 1776454819, 1779667416, 1955100553, 157405, "SRX23331822", "SRS20194274", "SRA1788753", "Iowa State University", "Iowa State University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-01-19", "Multi-stage", "Multi-stage", "Endothelium", "Cardiovascular System"], [30007, "SRR27663959", "SRX23331821", "SRS20194275", "SRP484810", "PRJNA1066877", "p65 signaling dynamics drive the developmental progression of hematopoietic stem and progenitor cells through cell cycle regulation", "GSE253758", "Transcriptome Analysis", "While hematopoietic stem and progenitor cells HSPCs and the signaling pathways that specify them have been well defined in vivo  deriving functional HSPCs from human pluripotent stem cells hPSCs is still an outstanding challenge in the stem cell field. This has impaired efforts to use patient specific HSPCs and their derivatives to treat leukemia  lymphoma  anemia  and solid cancers. Identifying the missing element to derive functional human HSPCs will be critical to advance these therapies. Here  we found that in contrast to in vitro protocols where signaling pathways are typically manipulated statically  the natural developmental progression of HSPC fate in the embryo requires a precise and temporally controlled oscillatory signaling dynamics.  Particularly  our work reveals that NF kB signaling works as an oscillatory clock that controls the developmental progression of HSPCs by driving phases of quiescence and proliferation precisely during embryonic development. This was revealed by live imaging of a custom NF kB zebrafish reporter line  in conjunction with transcriptomic profiling and precise temporal manipulations of the NF kB family member p65  the driver of these signaling events. We also show that in vitro protocols of human hematopoietic differentiation from iPSCs depend on initial pro inflammatory signaling activation. In summary  our results uncover the functional role of pro inflammatory signaling during HSPC specification  revealed their oscillatory dynamics  and define this signaling pathway as the main driver of HSPC fate progression. The integration of these dynamics in vitro will be fundamental to achieve the long standing goal of generating and expanding patient derived functional HSPCs. Overall design: To gain insights into how NF kB in endothelium was contributing to HSPC specification  NFKB+ or NFKB  endothelial cells kdrl+ were sorted and collected from 22hpf zebrafish embryos in triplicate and subject to RNA seq.", null, "pubmed:39242546", null, "NFKB   biol rep 2", "GSM8027551", null, "tissue:endothelial cells|cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB  sorted|geo loc name:missing|collection date:missing", "NFKB   biol rep 2", "Data was analyzed by ROSALIND\u00ae https://rosalind.bio/  with a HyperScale architecture developed by ROSALIND  Inc. San Diego  CA. Reads were trimmed using cutadapt. Reads were aligned to the Danio rerio genome build danRer10 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression RLE using DESeq2. Assembly: danRer10 Supplementary files format and content: comma delimited text files include fold change  p values  adjusted p values  and normalized abundance values per sample for each gene", "endothelial cells", "22hpf NFKB:d2eGFP x kdrl:mCherry zebrafish embryos were screened with Leica M165FC stereomicroscope  dechorionated with pronase Millipore Sigma; 11459643001  anesthetized in 1% tricaine Pentair; TRS5 and dissociated. Specifically  the trunk region of each embryo was surgically isolated posterior to the yolk ball and anterior to the urogenital canal using a scalpel. The collected tissue was then gently vortexed at 28C for 5 20 mins with 50 \u00b5g/ml Liberase TM Millipore Sigma: 5401127001 in Dulbecco\u2032s Phosphate Buffered Saline solution with Ca2+ and Mg2+ Millipore Sigma  D8662. The resulting cell suspension was filtered through 30 \u00b5m nylon mesh Fisher Scientific; NC9084441 using a 21 gauge syringe Fisher Scientific; BD 309624 and stained with SYTOX\u2122 Red Life Technologies; S34859 to exclude dead cells. Kdrl+/NFKB  and kdrl+/NFKB+ cells were each sorted and collected with BD FACS Aria III. 7 000 cells per sample were collected by FACS in Eppendorf tubes containing 250 \u00b5l of RLT buffer.", "RNA was then isolated and purified with RNeasy\u00ae Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer\u2019s instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.", "Zebrafish Danio rerio embryos and adults were mated  staged  raised  and processed in a circulating aquarium system maintained at 26 \u00b0C on a 14 hr light/10 hr dark cycle.", "cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB  sorted", "GSM8027551", "GSM8027551: NFKB   biol rep 2; Danio rerio; RNA Seq", "GSM8027551 r1", "GSM8027551", "1", "RNA was then isolated and purified with RNeasy\u00ae Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer's instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484810", null, "loader:fastq load.py", "5-RNA-0901_S5_L001_R1_001.fastq.gz", "fastq", 8077393600.0, 80773936.0, "GSM8027551 r1", "0:100", "A:2195547260;C:1863472493;G:1887149224;T:2131055526;N:169097", 100, null, null, null, 2195547260, 1863472493, 1887149224, 2131055526, 169097, "SRX23331821", "SRS20194275", "SRA1788753", "Iowa State University", "Iowa State University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-01-19", "Multi-stage", "Multi-stage", "Endothelium", "Cardiovascular System"], [30008, "SRR27663960", "SRX23331820", "SRS20194273", "SRP484810", "PRJNA1066877", "p65 signaling dynamics drive the developmental progression of hematopoietic stem and progenitor cells through cell cycle regulation", "GSE253758", "Transcriptome Analysis", "While hematopoietic stem and progenitor cells HSPCs and the signaling pathways that specify them have been well defined in vivo  deriving functional HSPCs from human pluripotent stem cells hPSCs is still an outstanding challenge in the stem cell field. This has impaired efforts to use patient specific HSPCs and their derivatives to treat leukemia  lymphoma  anemia  and solid cancers. Identifying the missing element to derive functional human HSPCs will be critical to advance these therapies. Here  we found that in contrast to in vitro protocols where signaling pathways are typically manipulated statically  the natural developmental progression of HSPC fate in the embryo requires a precise and temporally controlled oscillatory signaling dynamics.  Particularly  our work reveals that NF kB signaling works as an oscillatory clock that controls the developmental progression of HSPCs by driving phases of quiescence and proliferation precisely during embryonic development. This was revealed by live imaging of a custom NF kB zebrafish reporter line  in conjunction with transcriptomic profiling and precise temporal manipulations of the NF kB family member p65  the driver of these signaling events. We also show that in vitro protocols of human hematopoietic differentiation from iPSCs depend on initial pro inflammatory signaling activation. In summary  our results uncover the functional role of pro inflammatory signaling during HSPC specification  revealed their oscillatory dynamics  and define this signaling pathway as the main driver of HSPC fate progression. The integration of these dynamics in vitro will be fundamental to achieve the long standing goal of generating and expanding patient derived functional HSPCs. Overall design: To gain insights into how NF kB in endothelium was contributing to HSPC specification  NFKB+ or NFKB  endothelial cells kdrl+ were sorted and collected from 22hpf zebrafish embryos in triplicate and subject to RNA seq.", null, "pubmed:39242546", null, "NFKB   biol rep 1", "GSM8027550", null, "tissue:endothelial cells|cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB  sorted|geo loc name:missing|collection date:missing", "NFKB   biol rep 1", "Data was analyzed by ROSALIND\u00ae https://rosalind.bio/  with a HyperScale architecture developed by ROSALIND  Inc. San Diego  CA. Reads were trimmed using cutadapt. Reads were aligned to the Danio rerio genome build danRer10 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression RLE using DESeq2. Assembly: danRer10 Supplementary files format and content: comma delimited text files include fold change  p values  adjusted p values  and normalized abundance values per sample for each gene", "endothelial cells", "22hpf NFKB:d2eGFP x kdrl:mCherry zebrafish embryos were screened with Leica M165FC stereomicroscope  dechorionated with pronase Millipore Sigma; 11459643001  anesthetized in 1% tricaine Pentair; TRS5 and dissociated. Specifically  the trunk region of each embryo was surgically isolated posterior to the yolk ball and anterior to the urogenital canal using a scalpel. The collected tissue was then gently vortexed at 28C for 5 20 mins with 50 \u00b5g/ml Liberase TM Millipore Sigma: 5401127001 in Dulbecco\u2032s Phosphate Buffered Saline solution with Ca2+ and Mg2+ Millipore Sigma  D8662. The resulting cell suspension was filtered through 30 \u00b5m nylon mesh Fisher Scientific; NC9084441 using a 21 gauge syringe Fisher Scientific; BD 309624 and stained with SYTOX\u2122 Red Life Technologies; S34859 to exclude dead cells. Kdrl+/NFKB  and kdrl+/NFKB+ cells were each sorted and collected with BD FACS Aria III. 7 000 cells per sample were collected by FACS in Eppendorf tubes containing 250 \u00b5l of RLT buffer.", "RNA was then isolated and purified with RNeasy\u00ae Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer\u2019s instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.", "Zebrafish Danio rerio embryos and adults were mated  staged  raised  and processed in a circulating aquarium system maintained at 26 \u00b0C on a 14 hr light/10 hr dark cycle.", "cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB  sorted", "GSM8027550", "GSM8027550: NFKB   biol rep 1; Danio rerio; RNA Seq", "GSM8027550 r1", "GSM8027550", "1", "RNA was then isolated and purified with RNeasy\u00ae Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer's instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484810", null, "loader:fastq load.py", "4-RNA-1001_S4_L001_R1_001.fastq.gz", "fastq", 6536957300.0, 65369573.0, "GSM8027550 r1", "0:100", "A:1764502914;C:1531091007;G:1533764634;T:1707464708;N:134037", 100, null, null, null, 1764502914, 1531091007, 1533764634, 1707464708, 134037, "SRX23331820", "SRS20194273", "SRA1788753", "Iowa State University", "Iowa State University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-01-19", "Multi-stage", "Multi-stage", "Endothelium", "Cardiovascular System"], [30009, "SRR27663961", "SRX23331819", "SRS20194272", "SRP484810", "PRJNA1066877", "p65 signaling dynamics drive the developmental progression of hematopoietic stem and progenitor cells through cell cycle regulation", "GSE253758", "Transcriptome Analysis", "While hematopoietic stem and progenitor cells HSPCs and the signaling pathways that specify them have been well defined in vivo  deriving functional HSPCs from human pluripotent stem cells hPSCs is still an outstanding challenge in the stem cell field. This has impaired efforts to use patient specific HSPCs and their derivatives to treat leukemia  lymphoma  anemia  and solid cancers. Identifying the missing element to derive functional human HSPCs will be critical to advance these therapies. Here  we found that in contrast to in vitro protocols where signaling pathways are typically manipulated statically  the natural developmental progression of HSPC fate in the embryo requires a precise and temporally controlled oscillatory signaling dynamics.  Particularly  our work reveals that NF kB signaling works as an oscillatory clock that controls the developmental progression of HSPCs by driving phases of quiescence and proliferation precisely during embryonic development. This was revealed by live imaging of a custom NF kB zebrafish reporter line  in conjunction with transcriptomic profiling and precise temporal manipulations of the NF kB family member p65  the driver of these signaling events. We also show that in vitro protocols of human hematopoietic differentiation from iPSCs depend on initial pro inflammatory signaling activation. In summary  our results uncover the functional role of pro inflammatory signaling during HSPC specification  revealed their oscillatory dynamics  and define this signaling pathway as the main driver of HSPC fate progression. The integration of these dynamics in vitro will be fundamental to achieve the long standing goal of generating and expanding patient derived functional HSPCs. Overall design: To gain insights into how NF kB in endothelium was contributing to HSPC specification  NFKB+ or NFKB  endothelial cells kdrl+ were sorted and collected from 22hpf zebrafish embryos in triplicate and subject to RNA seq.", null, "pubmed:39242546", null, "NFKB+  biol rep 3", "GSM8027549", null, "tissue:endothelial cells|cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB+ sorted|geo loc name:missing|collection date:missing", "NFKB+  biol rep 3", "Data was analyzed by ROSALIND\u00ae https://rosalind.bio/  with a HyperScale architecture developed by ROSALIND  Inc. San Diego  CA. Reads were trimmed using cutadapt. Reads were aligned to the Danio rerio genome build danRer10 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression RLE using DESeq2. Assembly: danRer10 Supplementary files format and content: comma delimited text files include fold change  p values  adjusted p values  and normalized abundance values per sample for each gene", "endothelial cells", "22hpf NFKB:d2eGFP x kdrl:mCherry zebrafish embryos were screened with Leica M165FC stereomicroscope  dechorionated with pronase Millipore Sigma; 11459643001  anesthetized in 1% tricaine Pentair; TRS5 and dissociated. Specifically  the trunk region of each embryo was surgically isolated posterior to the yolk ball and anterior to the urogenital canal using a scalpel. The collected tissue was then gently vortexed at 28C for 5 20 mins with 50 \u00b5g/ml Liberase TM Millipore Sigma: 5401127001 in Dulbecco\u2032s Phosphate Buffered Saline solution with Ca2+ and Mg2+ Millipore Sigma  D8662. The resulting cell suspension was filtered through 30 \u00b5m nylon mesh Fisher Scientific; NC9084441 using a 21 gauge syringe Fisher Scientific; BD 309624 and stained with SYTOX\u2122 Red Life Technologies; S34859 to exclude dead cells. Kdrl+/NFKB  and kdrl+/NFKB+ cells were each sorted and collected with BD FACS Aria III. 7 000 cells per sample were collected by FACS in Eppendorf tubes containing 250 \u00b5l of RLT buffer.", "RNA was then isolated and purified with RNeasy\u00ae Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer\u2019s instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.", "Zebrafish Danio rerio embryos and adults were mated  staged  raised  and processed in a circulating aquarium system maintained at 26 \u00b0C on a 14 hr light/10 hr dark cycle.", "cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB+ sorted", "GSM8027549", "GSM8027549: NFKB+  biol rep 3; Danio rerio; RNA Seq", "GSM8027549 r1", "GSM8027549", "1", "RNA was then isolated and purified with RNeasy\u00ae Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer's instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484810", null, "loader:fastq load.py", "3-RNA-1001_S3_L001_R1_001.fastq.gz", "fastq", 10375249700.0, 103752497.0, "GSM8027549 r1", "0:100", "A:2873369145;C:2335823279;G:2356855554;T:2808985435;N:216287", 100, null, null, null, 2873369145, 2335823279, 2356855554, 2808985435, 216287, "SRX23331819", "SRS20194272", "SRA1788753", "Iowa State University", "Iowa State University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-01-19", "Multi-stage", "Multi-stage", "Endothelium", "Cardiovascular System"], [30010, "SRR27663962", "SRX23331818", "SRS20194271", "SRP484810", "PRJNA1066877", "p65 signaling dynamics drive the developmental progression of hematopoietic stem and progenitor cells through cell cycle regulation", "GSE253758", "Transcriptome Analysis", "While hematopoietic stem and progenitor cells HSPCs and the signaling pathways that specify them have been well defined in vivo  deriving functional HSPCs from human pluripotent stem cells hPSCs is still an outstanding challenge in the stem cell field. This has impaired efforts to use patient specific HSPCs and their derivatives to treat leukemia  lymphoma  anemia  and solid cancers. Identifying the missing element to derive functional human HSPCs will be critical to advance these therapies. Here  we found that in contrast to in vitro protocols where signaling pathways are typically manipulated statically  the natural developmental progression of HSPC fate in the embryo requires a precise and temporally controlled oscillatory signaling dynamics.  Particularly  our work reveals that NF kB signaling works as an oscillatory clock that controls the developmental progression of HSPCs by driving phases of quiescence and proliferation precisely during embryonic development. This was revealed by live imaging of a custom NF kB zebrafish reporter line  in conjunction with transcriptomic profiling and precise temporal manipulations of the NF kB family member p65  the driver of these signaling events. We also show that in vitro protocols of human hematopoietic differentiation from iPSCs depend on initial pro inflammatory signaling activation. In summary  our results uncover the functional role of pro inflammatory signaling during HSPC specification  revealed their oscillatory dynamics  and define this signaling pathway as the main driver of HSPC fate progression. The integration of these dynamics in vitro will be fundamental to achieve the long standing goal of generating and expanding patient derived functional HSPCs. Overall design: To gain insights into how NF kB in endothelium was contributing to HSPC specification  NFKB+ or NFKB  endothelial cells kdrl+ were sorted and collected from 22hpf zebrafish embryos in triplicate and subject to RNA seq.", null, "pubmed:39242546", null, "NFKB+  biol rep 2", "GSM8027548", null, "tissue:endothelial cells|cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB+ sorted|geo loc name:missing|collection date:missing", "NFKB+  biol rep 2", "Data was analyzed by ROSALIND\u00ae https://rosalind.bio/  with a HyperScale architecture developed by ROSALIND  Inc. San Diego  CA. Reads were trimmed using cutadapt. Reads were aligned to the Danio rerio genome build danRer10 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression RLE using DESeq2. Assembly: danRer10 Supplementary files format and content: comma delimited text files include fold change  p values  adjusted p values  and normalized abundance values per sample for each gene", "endothelial cells", "22hpf NFKB:d2eGFP x kdrl:mCherry zebrafish embryos were screened with Leica M165FC stereomicroscope  dechorionated with pronase Millipore Sigma; 11459643001  anesthetized in 1% tricaine Pentair; TRS5 and dissociated. Specifically  the trunk region of each embryo was surgically isolated posterior to the yolk ball and anterior to the urogenital canal using a scalpel. The collected tissue was then gently vortexed at 28C for 5 20 mins with 50 \u00b5g/ml Liberase TM Millipore Sigma: 5401127001 in Dulbecco\u2032s Phosphate Buffered Saline solution with Ca2+ and Mg2+ Millipore Sigma  D8662. The resulting cell suspension was filtered through 30 \u00b5m nylon mesh Fisher Scientific; NC9084441 using a 21 gauge syringe Fisher Scientific; BD 309624 and stained with SYTOX\u2122 Red Life Technologies; S34859 to exclude dead cells. Kdrl+/NFKB  and kdrl+/NFKB+ cells were each sorted and collected with BD FACS Aria III. 7 000 cells per sample were collected by FACS in Eppendorf tubes containing 250 \u00b5l of RLT buffer.", "RNA was then isolated and purified with RNeasy\u00ae Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer\u2019s instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.", "Zebrafish Danio rerio embryos and adults were mated  staged  raised  and processed in a circulating aquarium system maintained at 26 \u00b0C on a 14 hr light/10 hr dark cycle.", "cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB+ sorted", "GSM8027548", "GSM8027548: NFKB+  biol rep 2; Danio rerio; RNA Seq", "GSM8027548 r1", "GSM8027548", "1", "RNA was then isolated and purified with RNeasy\u00ae Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer's instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484810", null, "loader:fastq load.py", "2-RNA-1001_S2_L001_R1_001.fastq.gz", "fastq", 5743794100.0, 57437941.0, "GSM8027548 r1", "0:100", "A:1588561398;C:1297479370;G:1310669617;T:1546965673;N:118042", 100, null, null, null, 1588561398, 1297479370, 1310669617, 1546965673, 118042, "SRX23331818", "SRS20194271", "SRA1788753", "Iowa State University", "Iowa State University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-01-19", "Multi-stage", "Multi-stage", "Endothelium", "Cardiovascular System"], [30011, "SRR27663963", "SRX23331817", "SRS20194270", "SRP484810", "PRJNA1066877", "p65 signaling dynamics drive the developmental progression of hematopoietic stem and progenitor cells through cell cycle regulation", "GSE253758", "Transcriptome Analysis", "While hematopoietic stem and progenitor cells HSPCs and the signaling pathways that specify them have been well defined in vivo  deriving functional HSPCs from human pluripotent stem cells hPSCs is still an outstanding challenge in the stem cell field. This has impaired efforts to use patient specific HSPCs and their derivatives to treat leukemia  lymphoma  anemia  and solid cancers. Identifying the missing element to derive functional human HSPCs will be critical to advance these therapies. Here  we found that in contrast to in vitro protocols where signaling pathways are typically manipulated statically  the natural developmental progression of HSPC fate in the embryo requires a precise and temporally controlled oscillatory signaling dynamics.  Particularly  our work reveals that NF kB signaling works as an oscillatory clock that controls the developmental progression of HSPCs by driving phases of quiescence and proliferation precisely during embryonic development. This was revealed by live imaging of a custom NF kB zebrafish reporter line  in conjunction with transcriptomic profiling and precise temporal manipulations of the NF kB family member p65  the driver of these signaling events. We also show that in vitro protocols of human hematopoietic differentiation from iPSCs depend on initial pro inflammatory signaling activation. In summary  our results uncover the functional role of pro inflammatory signaling during HSPC specification  revealed their oscillatory dynamics  and define this signaling pathway as the main driver of HSPC fate progression. The integration of these dynamics in vitro will be fundamental to achieve the long standing goal of generating and expanding patient derived functional HSPCs. Overall design: To gain insights into how NF kB in endothelium was contributing to HSPC specification  NFKB+ or NFKB  endothelial cells kdrl+ were sorted and collected from 22hpf zebrafish embryos in triplicate and subject to RNA seq.", null, "pubmed:39242546", null, "NFKB+  biol rep 1", "GSM8027547", null, "tissue:endothelial cells|cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB+ sorted|geo loc name:missing|collection date:missing", "NFKB+  biol rep 1", "Data was analyzed by ROSALIND\u00ae https://rosalind.bio/  with a HyperScale architecture developed by ROSALIND  Inc. San Diego  CA. Reads were trimmed using cutadapt. Reads were aligned to the Danio rerio genome build danRer10 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression RLE using DESeq2. Assembly: danRer10 Supplementary files format and content: comma delimited text files include fold change  p values  adjusted p values  and normalized abundance values per sample for each gene", "endothelial cells", "22hpf NFKB:d2eGFP x kdrl:mCherry zebrafish embryos were screened with Leica M165FC stereomicroscope  dechorionated with pronase Millipore Sigma; 11459643001  anesthetized in 1% tricaine Pentair; TRS5 and dissociated. Specifically  the trunk region of each embryo was surgically isolated posterior to the yolk ball and anterior to the urogenital canal using a scalpel. The collected tissue was then gently vortexed at 28C for 5 20 mins with 50 \u00b5g/ml Liberase TM Millipore Sigma: 5401127001 in Dulbecco\u2032s Phosphate Buffered Saline solution with Ca2+ and Mg2+ Millipore Sigma  D8662. The resulting cell suspension was filtered through 30 \u00b5m nylon mesh Fisher Scientific; NC9084441 using a 21 gauge syringe Fisher Scientific; BD 309624 and stained with SYTOX\u2122 Red Life Technologies; S34859 to exclude dead cells. Kdrl+/NFKB  and kdrl+/NFKB+ cells were each sorted and collected with BD FACS Aria III. 7 000 cells per sample were collected by FACS in Eppendorf tubes containing 250 \u00b5l of RLT buffer.", "RNA was then isolated and purified with RNeasy\u00ae Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer\u2019s instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.", "Zebrafish Danio rerio embryos and adults were mated  staged  raised  and processed in a circulating aquarium system maintained at 26 \u00b0C on a 14 hr light/10 hr dark cycle.", "cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB+ sorted", "GSM8027547", "GSM8027547: NFKB+  biol rep 1; Danio rerio; RNA Seq", "GSM8027547 r1", "GSM8027547", "1", "RNA was then isolated and purified with RNeasy\u00ae Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer's instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP484810", null, "loader:fastq load.py", "1-RNA-0917_S1_L001_R1_001.fastq.gz", "fastq", 6201542500.0, 62015425.0, "GSM8027547 r1", "0:100", "A:1696049302;C:1431941155;G:1441395671;T:1632027072;N:129300", 100, null, null, null, 1696049302, 1431941155, 1441395671, 1632027072, 129300, "SRX23331817", "SRS20194270", "SRA1788753", "Iowa State University", "Iowa State University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "United States", "2024-01-19", "Multi-stage", "Multi-stage", "Endothelium", "Cardiovascular System"], [30512, "SRR27764782", "SRX23429747", "SRS20284188", "SRP486526", "PRJNA1070616", "Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response", "GSE254466", "Transcriptome Analysis", "The oxidative phosphorylation OXPHOS system is dynamic and the respiratory complexes RCs coexist with super assembled quaternary structures called supercomplexes SCs. How assembly occurs and the physiological role of supercomplex assembly is still under intensive investigation. The Cox7a family member Cox7a2l  also known as Scaf1  promotes CIII CIV super assembly and energetic efficiency in zebrafish  mice  and humans. Here we studied the role of a second member of the Cox7a family  Cox7a1 in SC assembly and striated muscle physiology. We found that this protein drives CIV homodimer formation  which increases CIV activity. The substantial reduction in CIV2 formation led to a profound metabolic rearrangement with a consequent non pathological loss of skeletal muscle performance. Ablation of Cox7a1 also rewired heart metabolism.  Already in homeostatic conditions  cox7a1 /  hearts revealed a pro regenerative metabolic profile. While overall cardiac function was not affected  the absence of Cox7a1 altered the cardiac regenerative response. The effects of cox7a1 and cox7a2l loss of function on skeletal muscle and myocardium physiology and injury response were not identical  revealing that there is  a high specificity of Cox7a isoform in controlling OXPHOS assembly and striated muscle metabolism. While in both cases overall OXPHOS activity is modified  the loss of CIII CIV heterodimer formation or CIV homodimer formation have very distinct metabolic and physiological consequences  highlighting the complexity of OXPHOS function and the importance of cox7a1 in striated muscle maturation. Overall design: Adult zebrafish hearts for cox7a1 /  mutants and wildtype siblings were cryoinjured. 7 xxx post injury the cardiac ventrilces were extracted and RNA was extracted for RNA seq.  4 pools each comprising 5 ventricles were sequenced per condition.", null, "pubmed:38701784", null, "Cardiac ventricle  cox7a1 /   replicate 4", "GSM8042779", null, "source name:Cardiac Ventricle|tissue:Cardiac Ventricle|genotype:Cox7a mut|treatment:7days post cryoinjury|geo loc name:missing|collection date:missing", "Cardiac ventricle  cox7a1 /   replicate 4", "Data were quality checked with Fastqc and Multiqc Sequences were trimmed with fastp 2 pass alignment was performed with STAR Aligner reads were dounted using featurecounts Normalization and downstream analysis including differential expression analysis was performed in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: feature counts  tab seprated values", "Cardiac Ventricle", null, "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "tissue:Cardiac Ventricle|genotype:Cox7a mut|treatment:7days post cryoinjury", "GSM8042779", "GSM8042779: Cardiac ventricle  cox7a1 /   replicate 4; Danio rerio; RNA Seq", "GSM8042779 r1", "GSM8042779", "1", "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP486526", null, null, "KO_10_Directional_S8_R1_001.fastq.gz", "fastq", 8619450300.0, 86194503.0, "GSM8042779 r1", "0:100", "A:2183264320;C:2042597849;G:2002385828;T:2389908983;N:1293320", 100, null, null, null, 2183264320, 2042597849, 2002385828, 2389908983, 1293320, "SRX23429747", "SRS20284188", "SRA1793874", "University of Bern", "University of Bern", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-29", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [30513, "SRR27764783", "SRX23429746", "SRS20284187", "SRP486526", "PRJNA1070616", "Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response", "GSE254466", "Transcriptome Analysis", "The oxidative phosphorylation OXPHOS system is dynamic and the respiratory complexes RCs coexist with super assembled quaternary structures called supercomplexes SCs. How assembly occurs and the physiological role of supercomplex assembly is still under intensive investigation. The Cox7a family member Cox7a2l  also known as Scaf1  promotes CIII CIV super assembly and energetic efficiency in zebrafish  mice  and humans. Here we studied the role of a second member of the Cox7a family  Cox7a1 in SC assembly and striated muscle physiology. We found that this protein drives CIV homodimer formation  which increases CIV activity. The substantial reduction in CIV2 formation led to a profound metabolic rearrangement with a consequent non pathological loss of skeletal muscle performance. Ablation of Cox7a1 also rewired heart metabolism.  Already in homeostatic conditions  cox7a1 /  hearts revealed a pro regenerative metabolic profile. While overall cardiac function was not affected  the absence of Cox7a1 altered the cardiac regenerative response. The effects of cox7a1 and cox7a2l loss of function on skeletal muscle and myocardium physiology and injury response were not identical  revealing that there is  a high specificity of Cox7a isoform in controlling OXPHOS assembly and striated muscle metabolism. While in both cases overall OXPHOS activity is modified  the loss of CIII CIV heterodimer formation or CIV homodimer formation have very distinct metabolic and physiological consequences  highlighting the complexity of OXPHOS function and the importance of cox7a1 in striated muscle maturation. Overall design: Adult zebrafish hearts for cox7a1 /  mutants and wildtype siblings were cryoinjured. 7 xxx post injury the cardiac ventrilces were extracted and RNA was extracted for RNA seq.  4 pools each comprising 5 ventricles were sequenced per condition.", null, "pubmed:38701784", null, "Cardiac ventricle  cox7a1 /   replicate 3", "GSM8042778", null, "source name:Cardiac Ventricle|tissue:Cardiac Ventricle|genotype:Cox7a mut|treatment:7days post cryoinjury|geo loc name:missing|collection date:missing", "Cardiac ventricle  cox7a1 /   replicate 3", "Data were quality checked with Fastqc and Multiqc Sequences were trimmed with fastp 2 pass alignment was performed with STAR Aligner reads were dounted using featurecounts Normalization and downstream analysis including differential expression analysis was performed in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: feature counts  tab seprated values", "Cardiac Ventricle", null, "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "tissue:Cardiac Ventricle|genotype:Cox7a mut|treatment:7days post cryoinjury", "GSM8042778", "GSM8042778: Cardiac ventricle  cox7a1 /   replicate 3; Danio rerio; RNA Seq", "GSM8042778 r1", "GSM8042778", "1", "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP486526", null, null, "KO_9_Directional_S7_R1_001.fastq.gz", "fastq", 6466746100.0, 64667461.0, "GSM8042778 r1", "0:100", "A:1708351950;C:1464168743;G:1452219209;T:1841033764;N:972434", 100, null, null, null, 1708351950, 1464168743, 1452219209, 1841033764, 972434, "SRX23429746", "SRS20284187", "SRA1793874", "University of Bern", "University of Bern", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-29", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [30514, "SRR27764784", "SRX23429745", "SRS20284186", "SRP486526", "PRJNA1070616", "Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response", "GSE254466", "Transcriptome Analysis", "The oxidative phosphorylation OXPHOS system is dynamic and the respiratory complexes RCs coexist with super assembled quaternary structures called supercomplexes SCs. How assembly occurs and the physiological role of supercomplex assembly is still under intensive investigation. The Cox7a family member Cox7a2l  also known as Scaf1  promotes CIII CIV super assembly and energetic efficiency in zebrafish  mice  and humans. Here we studied the role of a second member of the Cox7a family  Cox7a1 in SC assembly and striated muscle physiology. We found that this protein drives CIV homodimer formation  which increases CIV activity. The substantial reduction in CIV2 formation led to a profound metabolic rearrangement with a consequent non pathological loss of skeletal muscle performance. Ablation of Cox7a1 also rewired heart metabolism.  Already in homeostatic conditions  cox7a1 /  hearts revealed a pro regenerative metabolic profile. While overall cardiac function was not affected  the absence of Cox7a1 altered the cardiac regenerative response. The effects of cox7a1 and cox7a2l loss of function on skeletal muscle and myocardium physiology and injury response were not identical  revealing that there is  a high specificity of Cox7a isoform in controlling OXPHOS assembly and striated muscle metabolism. While in both cases overall OXPHOS activity is modified  the loss of CIII CIV heterodimer formation or CIV homodimer formation have very distinct metabolic and physiological consequences  highlighting the complexity of OXPHOS function and the importance of cox7a1 in striated muscle maturation. Overall design: Adult zebrafish hearts for cox7a1 /  mutants and wildtype siblings were cryoinjured. 7 xxx post injury the cardiac ventrilces were extracted and RNA was extracted for RNA seq.  4 pools each comprising 5 ventricles were sequenced per condition.", null, "pubmed:38701784", null, "Cardiac ventricle  cox7a1 /   replicate 2", "GSM8042777", null, "source name:Cardiac Ventricle|tissue:Cardiac Ventricle|genotype:Cox7a mut|treatment:7days post cryoinjury|geo loc name:missing|collection date:missing", "Cardiac ventricle  cox7a1 /   replicate 2", "Data were quality checked with Fastqc and Multiqc Sequences were trimmed with fastp 2 pass alignment was performed with STAR Aligner reads were dounted using featurecounts Normalization and downstream analysis including differential expression analysis was performed in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: feature counts  tab seprated values", "Cardiac Ventricle", null, "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "tissue:Cardiac Ventricle|genotype:Cox7a mut|treatment:7days post cryoinjury", "GSM8042777", "GSM8042777: Cardiac ventricle  cox7a1 /   replicate 2; Danio rerio; RNA Seq", "GSM8042777 r1", "GSM8042777", "1", "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP486526", null, null, "KO_8_Directional_S6_R1_001.fastq.gz", "fastq", 6766795300.0, 67667953.0, "GSM8042777 r1", "0:100", "A:1803038642;C:1540664299;G:1518741633;T:1903355305;N:995421", 100, null, null, null, 1803038642, 1540664299, 1518741633, 1903355305, 995421, "SRX23429745", "SRS20284186", "SRA1793874", "University of Bern", "University of Bern", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-29", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [30515, "SRR27764785", "SRX23429744", "SRS20284185", "SRP486526", "PRJNA1070616", "Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response", "GSE254466", "Transcriptome Analysis", "The oxidative phosphorylation OXPHOS system is dynamic and the respiratory complexes RCs coexist with super assembled quaternary structures called supercomplexes SCs. How assembly occurs and the physiological role of supercomplex assembly is still under intensive investigation. The Cox7a family member Cox7a2l  also known as Scaf1  promotes CIII CIV super assembly and energetic efficiency in zebrafish  mice  and humans. Here we studied the role of a second member of the Cox7a family  Cox7a1 in SC assembly and striated muscle physiology. We found that this protein drives CIV homodimer formation  which increases CIV activity. The substantial reduction in CIV2 formation led to a profound metabolic rearrangement with a consequent non pathological loss of skeletal muscle performance. Ablation of Cox7a1 also rewired heart metabolism.  Already in homeostatic conditions  cox7a1 /  hearts revealed a pro regenerative metabolic profile. While overall cardiac function was not affected  the absence of Cox7a1 altered the cardiac regenerative response. The effects of cox7a1 and cox7a2l loss of function on skeletal muscle and myocardium physiology and injury response were not identical  revealing that there is  a high specificity of Cox7a isoform in controlling OXPHOS assembly and striated muscle metabolism. While in both cases overall OXPHOS activity is modified  the loss of CIII CIV heterodimer formation or CIV homodimer formation have very distinct metabolic and physiological consequences  highlighting the complexity of OXPHOS function and the importance of cox7a1 in striated muscle maturation. Overall design: Adult zebrafish hearts for cox7a1 /  mutants and wildtype siblings were cryoinjured. 7 xxx post injury the cardiac ventrilces were extracted and RNA was extracted for RNA seq.  4 pools each comprising 5 ventricles were sequenced per condition.", null, "pubmed:38701784", null, "Cardiac ventricle  cox7a1 /   replicate 1", "GSM8042776", null, "source name:Cardiac Ventricle|tissue:Cardiac Ventricle|genotype:Cox7a mut|treatment:7days post cryoinjury|geo loc name:missing|collection date:missing", "Cardiac ventricle  cox7a1 /   replicate 1", "Data were quality checked with Fastqc and Multiqc Sequences were trimmed with fastp 2 pass alignment was performed with STAR Aligner reads were dounted using featurecounts Normalization and downstream analysis including differential expression analysis was performed in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: feature counts  tab seprated values", "Cardiac Ventricle", null, "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "tissue:Cardiac Ventricle|genotype:Cox7a mut|treatment:7days post cryoinjury", "GSM8042776", "GSM8042776: Cardiac ventricle  cox7a1 /   replicate 1; Danio rerio; RNA Seq", "GSM8042776 r1", "GSM8042776", "1", "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP486526", null, null, "KO_7_Directional_S5_R1_001.fastq.gz", "fastq", 5583049300.0, 55830493.0, "GSM8042776 r1", "0:100", "A:1479820662;C:1265599242;G:1251078421;T:1585727832;N:823143", 100, null, null, null, 1479820662, 1265599242, 1251078421, 1585727832, 823143, "SRX23429744", "SRS20284185", "SRA1793874", "University of Bern", "University of Bern", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-29", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [30516, "SRR27764786", "SRX23429743", "SRS20284184", "SRP486526", "PRJNA1070616", "Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response", "GSE254466", "Transcriptome Analysis", "The oxidative phosphorylation OXPHOS system is dynamic and the respiratory complexes RCs coexist with super assembled quaternary structures called supercomplexes SCs. How assembly occurs and the physiological role of supercomplex assembly is still under intensive investigation. The Cox7a family member Cox7a2l  also known as Scaf1  promotes CIII CIV super assembly and energetic efficiency in zebrafish  mice  and humans. Here we studied the role of a second member of the Cox7a family  Cox7a1 in SC assembly and striated muscle physiology. We found that this protein drives CIV homodimer formation  which increases CIV activity. The substantial reduction in CIV2 formation led to a profound metabolic rearrangement with a consequent non pathological loss of skeletal muscle performance. Ablation of Cox7a1 also rewired heart metabolism.  Already in homeostatic conditions  cox7a1 /  hearts revealed a pro regenerative metabolic profile. While overall cardiac function was not affected  the absence of Cox7a1 altered the cardiac regenerative response. The effects of cox7a1 and cox7a2l loss of function on skeletal muscle and myocardium physiology and injury response were not identical  revealing that there is  a high specificity of Cox7a isoform in controlling OXPHOS assembly and striated muscle metabolism. While in both cases overall OXPHOS activity is modified  the loss of CIII CIV heterodimer formation or CIV homodimer formation have very distinct metabolic and physiological consequences  highlighting the complexity of OXPHOS function and the importance of cox7a1 in striated muscle maturation. Overall design: Adult zebrafish hearts for cox7a1 /  mutants and wildtype siblings were cryoinjured. 7 xxx post injury the cardiac ventrilces were extracted and RNA was extracted for RNA seq.  4 pools each comprising 5 ventricles were sequenced per condition.", null, "pubmed:38701784", null, "Cardiac ventricle  wt sibling  replicate 4", "GSM8042775", null, "source name:Cardiac Ventricle|tissue:Cardiac Ventricle|genotype:WT|treatment:7days post cryoinjury|geo loc name:missing|collection date:missing", "Cardiac ventricle  wt sibling  replicate 4", "Data were quality checked with Fastqc and Multiqc Sequences were trimmed with fastp 2 pass alignment was performed with STAR Aligner reads were dounted using featurecounts Normalization and downstream analysis including differential expression analysis was performed in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: feature counts  tab seprated values", "Cardiac Ventricle", null, "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "tissue:Cardiac Ventricle|genotype:WT|treatment:7days post cryoinjury", "GSM8042775", "GSM8042775: Cardiac ventricle  wt sibling  replicate 4; Danio rerio; RNA Seq", "GSM8042775 r1", "GSM8042775", "1", "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP486526", null, null, "WT_5_Directional_S4_R1_001.fastq.gz", "fastq", 6851217800.0, 68512178.0, "GSM8042775 r1", "0:100", "A:1837112549;C:1539284911;G:1515596368;T:1958221274;N:1002698", 100, null, null, null, 1837112549, 1539284911, 1515596368, 1958221274, 1002698, "SRX23429743", "SRS20284184", "SRA1793874", "University of Bern", "University of Bern", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-29", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [30517, "SRR27764787", "SRX23429742", "SRS20284183", "SRP486526", "PRJNA1070616", "Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response", "GSE254466", "Transcriptome Analysis", "The oxidative phosphorylation OXPHOS system is dynamic and the respiratory complexes RCs coexist with super assembled quaternary structures called supercomplexes SCs. How assembly occurs and the physiological role of supercomplex assembly is still under intensive investigation. The Cox7a family member Cox7a2l  also known as Scaf1  promotes CIII CIV super assembly and energetic efficiency in zebrafish  mice  and humans. Here we studied the role of a second member of the Cox7a family  Cox7a1 in SC assembly and striated muscle physiology. We found that this protein drives CIV homodimer formation  which increases CIV activity. The substantial reduction in CIV2 formation led to a profound metabolic rearrangement with a consequent non pathological loss of skeletal muscle performance. Ablation of Cox7a1 also rewired heart metabolism.  Already in homeostatic conditions  cox7a1 /  hearts revealed a pro regenerative metabolic profile. While overall cardiac function was not affected  the absence of Cox7a1 altered the cardiac regenerative response. The effects of cox7a1 and cox7a2l loss of function on skeletal muscle and myocardium physiology and injury response were not identical  revealing that there is  a high specificity of Cox7a isoform in controlling OXPHOS assembly and striated muscle metabolism. While in both cases overall OXPHOS activity is modified  the loss of CIII CIV heterodimer formation or CIV homodimer formation have very distinct metabolic and physiological consequences  highlighting the complexity of OXPHOS function and the importance of cox7a1 in striated muscle maturation. Overall design: Adult zebrafish hearts for cox7a1 /  mutants and wildtype siblings were cryoinjured. 7 xxx post injury the cardiac ventrilces were extracted and RNA was extracted for RNA seq.  4 pools each comprising 5 ventricles were sequenced per condition.", null, "pubmed:38701784", null, "Cardiac ventricle  wt sibling  replicate 3", "GSM8042774", null, "source name:Cardiac Ventricle|tissue:Cardiac Ventricle|genotype:WT|treatment:7days post cryoinjury|geo loc name:missing|collection date:missing", "Cardiac ventricle  wt sibling  replicate 3", "Data were quality checked with Fastqc and Multiqc Sequences were trimmed with fastp 2 pass alignment was performed with STAR Aligner reads were dounted using featurecounts Normalization and downstream analysis including differential expression analysis was performed in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: feature counts  tab seprated values", "Cardiac Ventricle", null, "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "tissue:Cardiac Ventricle|genotype:WT|treatment:7days post cryoinjury", "GSM8042774", "GSM8042774: Cardiac ventricle  wt sibling  replicate 3; Danio rerio; RNA Seq", "GSM8042774 r1", "GSM8042774", "1", "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP486526", null, null, "WT_3_Directional_S3_R1_001.fastq.gz", "fastq", 7036251700.0, 70362517.0, "GSM8042774 r1", "0:100", "A:1881612688;C:1574593657;G:1570342252;T:2008668471;N:1034632", 100, null, null, null, 1881612688, 1574593657, 1570342252, 2008668471, 1034632, "SRX23429742", "SRS20284183", "SRA1793874", "University of Bern", "University of Bern", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-29", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [30518, "SRR27764788", "SRX23429741", "SRS20284182", "SRP486526", "PRJNA1070616", "Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response", "GSE254466", "Transcriptome Analysis", "The oxidative phosphorylation OXPHOS system is dynamic and the respiratory complexes RCs coexist with super assembled quaternary structures called supercomplexes SCs. How assembly occurs and the physiological role of supercomplex assembly is still under intensive investigation. The Cox7a family member Cox7a2l  also known as Scaf1  promotes CIII CIV super assembly and energetic efficiency in zebrafish  mice  and humans. Here we studied the role of a second member of the Cox7a family  Cox7a1 in SC assembly and striated muscle physiology. We found that this protein drives CIV homodimer formation  which increases CIV activity. The substantial reduction in CIV2 formation led to a profound metabolic rearrangement with a consequent non pathological loss of skeletal muscle performance. Ablation of Cox7a1 also rewired heart metabolism.  Already in homeostatic conditions  cox7a1 /  hearts revealed a pro regenerative metabolic profile. While overall cardiac function was not affected  the absence of Cox7a1 altered the cardiac regenerative response. The effects of cox7a1 and cox7a2l loss of function on skeletal muscle and myocardium physiology and injury response were not identical  revealing that there is  a high specificity of Cox7a isoform in controlling OXPHOS assembly and striated muscle metabolism. While in both cases overall OXPHOS activity is modified  the loss of CIII CIV heterodimer formation or CIV homodimer formation have very distinct metabolic and physiological consequences  highlighting the complexity of OXPHOS function and the importance of cox7a1 in striated muscle maturation. Overall design: Adult zebrafish hearts for cox7a1 /  mutants and wildtype siblings were cryoinjured. 7 xxx post injury the cardiac ventrilces were extracted and RNA was extracted for RNA seq.  4 pools each comprising 5 ventricles were sequenced per condition.", null, "pubmed:38701784", null, "Cardiac ventricle  wt sibling  replicate 2", "GSM8042773", null, "source name:Cardiac Ventricle|tissue:Cardiac Ventricle|genotype:WT|treatment:7days post cryoinjury|geo loc name:missing|collection date:missing", "Cardiac ventricle  wt sibling  replicate 2", "Data were quality checked with Fastqc and Multiqc Sequences were trimmed with fastp 2 pass alignment was performed with STAR Aligner reads were dounted using featurecounts Normalization and downstream analysis including differential expression analysis was performed in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: feature counts  tab seprated values", "Cardiac Ventricle", null, "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "tissue:Cardiac Ventricle|genotype:WT|treatment:7days post cryoinjury", "GSM8042773", "GSM8042773: Cardiac ventricle  wt sibling  replicate 2; Danio rerio; RNA Seq", "GSM8042773 r1", "GSM8042773", "1", "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP486526", null, null, "WT_2_Directional_S2_R1_001.fastq.gz", "fastq", 6856428200.0, 68564282.0, "GSM8042773 r1", "0:100", "A:1790369167;C:1572129686;G:1566120109;T:1926782247;N:1026991", 100, null, null, null, 1790369167, 1572129686, 1566120109, 1926782247, 1026991, "SRX23429741", "SRS20284182", "SRA1793874", "University of Bern", "University of Bern", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-29", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [30519, "SRR27764789", "SRX23429740", "SRS20284181", "SRP486526", "PRJNA1070616", "Cox7a1 mediated CIV dimerization impacts skeletal muscle physiology and cardiac injury response", "GSE254466", "Transcriptome Analysis", "The oxidative phosphorylation OXPHOS system is dynamic and the respiratory complexes RCs coexist with super assembled quaternary structures called supercomplexes SCs. How assembly occurs and the physiological role of supercomplex assembly is still under intensive investigation. The Cox7a family member Cox7a2l  also known as Scaf1  promotes CIII CIV super assembly and energetic efficiency in zebrafish  mice  and humans. Here we studied the role of a second member of the Cox7a family  Cox7a1 in SC assembly and striated muscle physiology. We found that this protein drives CIV homodimer formation  which increases CIV activity. The substantial reduction in CIV2 formation led to a profound metabolic rearrangement with a consequent non pathological loss of skeletal muscle performance. Ablation of Cox7a1 also rewired heart metabolism.  Already in homeostatic conditions  cox7a1 /  hearts revealed a pro regenerative metabolic profile. While overall cardiac function was not affected  the absence of Cox7a1 altered the cardiac regenerative response. The effects of cox7a1 and cox7a2l loss of function on skeletal muscle and myocardium physiology and injury response were not identical  revealing that there is  a high specificity of Cox7a isoform in controlling OXPHOS assembly and striated muscle metabolism. While in both cases overall OXPHOS activity is modified  the loss of CIII CIV heterodimer formation or CIV homodimer formation have very distinct metabolic and physiological consequences  highlighting the complexity of OXPHOS function and the importance of cox7a1 in striated muscle maturation. Overall design: Adult zebrafish hearts for cox7a1 /  mutants and wildtype siblings were cryoinjured. 7 xxx post injury the cardiac ventrilces were extracted and RNA was extracted for RNA seq.  4 pools each comprising 5 ventricles were sequenced per condition.", null, "pubmed:38701784", null, "Cardiac ventricle  wt sibling  replicate 1", "GSM8042772", null, "source name:Cardiac Ventricle|tissue:Cardiac Ventricle|genotype:WT|treatment:7days post cryoinjury|geo loc name:missing|collection date:missing", "Cardiac ventricle  wt sibling  replicate 1", "Data were quality checked with Fastqc and Multiqc Sequences were trimmed with fastp 2 pass alignment was performed with STAR Aligner reads were dounted using featurecounts Normalization and downstream analysis including differential expression analysis was performed in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: feature counts  tab seprated values", "Cardiac Ventricle", null, "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "tissue:Cardiac Ventricle|genotype:WT|treatment:7days post cryoinjury", "GSM8042772", "GSM8042772: Cardiac ventricle  wt sibling  replicate 1; Danio rerio; RNA Seq", "GSM8042772 r1", "GSM8042772", "1", "4 pools each comprising 5 ventricles were sequenced per condition. Libraries for RNA seq were prepared using the \"NEBNext Ultra II Directional RNA library prep Kit for Illumina\" following manufacturer\u00b4s protocol", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP486526", null, null, "WT_1_Directional_S1_R1_001.fastq.gz", "fastq", 7089416800.0, 70894168.0, "GSM8042772 r1", "0:100", "A:1855346146;C:1626812736;G:1599932420;T:2006283874;N:1041624", 100, null, null, null, 1855346146, 1626812736, 1599932420, 2006283874, 1041624, "SRX23429740", "SRS20284181", "SRA1793874", "University of Bern", "University of Bern", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "nebnext", "bulk", "unknown", "unknown", null, "Switzerland", "2024-01-29", "Undetermined", "Adult", "Heart", "Cardiovascular System"], [31896, "SRR28745432", "SRX24311225", "SRS21073227", "SRP502845", "PRJNA1102356", "flt1 inactivation promotes zebrafish cardiac regeneration by enhancing endothelial activity and limiting the fibrotic response", "GSE264406", "Transcriptome Analysis", "VEGFA administration has been explored as a pro angiogenic therapy for cardiovascular diseases including heart failure for several years; however  many challenges remain.  Here we investigate a different approach to augmenting VEGFA bioavailability  one that achieves more physiological VEGFA concentrations by deleting VEGFR1/FLT1  a VEGFA decoy receptor.  We find that  following cryoinjury  zebrafish flt1 mutant hearts display enhanced coronary revascularization and endocardial expansion  increased cardiomyocyte dedifferentiation and proliferation  and decreased scarring.  Suppressing Vegfa signaling in flt1 mutants abrogates the beneficial effects of flt1 deletion.  Transcriptomic analyses of cryoinjured flt1 mutant hearts revealed enhanced endothelial MAPK/ERK signaling and downregulation of the transcription factor gene egr3.  Using genetic tools  we observe egr3 upregulation in the regenerating endocardium and find that Egr3 promotes myofibroblast differentiation.  These data suggest that with enhanced VEGFA bioavailability  the cardiac endothelium limits myofibroblast differentiation via egr3 downregulation  thereby providing a more permissive microenvironment for cardiomyocyte xxx post injury. Overall design: Comparative gene expression analysis between cryoinjured wild type zebrafish ventricles and flt1 mutant ventricles at 96 hours post cryoinjury.", null, "pubmed:39612288", null, "wild type heart  96 hours post cryoinjury 3", "GSM8217704", null, "source name:heart ventricle border z1 and injured area|tissue:heart ventricle border z1 and injured area|genotype:wild type|treatment:cardiac cryoinjury|geo loc name:missing|collection date:missing", "wild type heart  96 hours post cryoinjury 3", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Aligned reads were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.36.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: danRer11 Supplementary files format and content: library size normlized count matrix", "heart ventricle border zone and injured area", null, "A pool of 5 ventricles was used per biological replicate. Total RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase Free DNase Set  Qiagen 4\u00b5g of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture\u2019s protocol Vazyme.", null, "tissue:heart ventricle border z1 and injured area|genotype:wild type|treatment:cardiac cryoinjury", "GSM8217704", "GSM8217704: wild type heart  96 hours post cryoinjury 3; Danio rerio; RNA Seq", "GSM8217704 r1", "GSM8217704", "1", "A pool of 5 ventricles was used per biological replicate. Total RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase Free DNase Set  Qiagen 4\u00b5g of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture's protocol Vazyme.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP502845", null, "loader:fastq load.py", "E23_4173_Armaad_Lib_WT3_R1.fastq.gz", "fastq", 3257983192.0, 47556048.0, "GSM8217704 r1", "0:68.51", "A:848972796;C:741588101;G:760680137;T:905607069;N:1135089", 68, null, null, null, 848972796, 741588101, 760680137, 905607069, 1135089, "SRX24311225", "SRS21073227", "SRA1849558", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.94185, null, 0.087, null, 0.72478, null, 0.50388, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-04-19", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [31897, "SRR28745433", "SRX24311224", "SRS21073229", "SRP502845", "PRJNA1102356", "flt1 inactivation promotes zebrafish cardiac regeneration by enhancing endothelial activity and limiting the fibrotic response", "GSE264406", "Transcriptome Analysis", "VEGFA administration has been explored as a pro angiogenic therapy for cardiovascular diseases including heart failure for several years; however  many challenges remain.  Here we investigate a different approach to augmenting VEGFA bioavailability  one that achieves more physiological VEGFA concentrations by deleting VEGFR1/FLT1  a VEGFA decoy receptor.  We find that  following cryoinjury  zebrafish flt1 mutant hearts display enhanced coronary revascularization and endocardial expansion  increased cardiomyocyte dedifferentiation and proliferation  and decreased scarring.  Suppressing Vegfa signaling in flt1 mutants abrogates the beneficial effects of flt1 deletion.  Transcriptomic analyses of cryoinjured flt1 mutant hearts revealed enhanced endothelial MAPK/ERK signaling and downregulation of the transcription factor gene egr3.  Using genetic tools  we observe egr3 upregulation in the regenerating endocardium and find that Egr3 promotes myofibroblast differentiation.  These data suggest that with enhanced VEGFA bioavailability  the cardiac endothelium limits myofibroblast differentiation via egr3 downregulation  thereby providing a more permissive microenvironment for cardiomyocyte xxx post injury. Overall design: Comparative gene expression analysis between cryoinjured wild type zebrafish ventricles and flt1 mutant ventricles at 96 hours post cryoinjury.", null, "pubmed:39612288", null, "wild type heart  96 hours post cryoinjury 2", "GSM8217703", null, "source name:heart ventricle border z1 and injured area|tissue:heart ventricle border z1 and injured area|genotype:wild type|treatment:cardiac cryoinjury|geo loc name:missing|collection date:missing", "wild type heart  96 hours post cryoinjury 2", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Aligned reads were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.36.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: danRer11 Supplementary files format and content: library size normlized count matrix", "heart ventricle border zone and injured area", null, "A pool of 5 ventricles was used per biological replicate. Total RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase Free DNase Set  Qiagen 4\u00b5g of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture\u2019s protocol Vazyme.", null, "tissue:heart ventricle border z1 and injured area|genotype:wild type|treatment:cardiac cryoinjury", "GSM8217703", "GSM8217703: wild type heart  96 hours post cryoinjury 2; Danio rerio; RNA Seq", "GSM8217703 r1", "GSM8217703", "1", "A pool of 5 ventricles was used per biological replicate. Total RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase Free DNase Set  Qiagen 4\u00b5g of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture's protocol Vazyme.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP502845", null, "loader:fastq load.py", "E23_4173_Armaad_Lib_WT2_R1.fastq.gz", "fastq", 3864619254.0, 56519751.0, "GSM8217703 r1", "0:68.38", "A:1003402543;C:880721584;G:903469106;T:1075304136;N:1721885", 68, null, null, null, 1003402543, 880721584, 903469106, 1075304136, 1721885, "SRX24311224", "SRS21073229", "SRA1849558", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.93928, null, 0.08915, null, 0.72348, null, 0.49993, null, 71, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-04-19", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [31898, "SRR28745434", "SRX24311223", "SRS21073228", "SRP502845", "PRJNA1102356", "flt1 inactivation promotes zebrafish cardiac regeneration by enhancing endothelial activity and limiting the fibrotic response", "GSE264406", "Transcriptome Analysis", "VEGFA administration has been explored as a pro angiogenic therapy for cardiovascular diseases including heart failure for several years; however  many challenges remain.  Here we investigate a different approach to augmenting VEGFA bioavailability  one that achieves more physiological VEGFA concentrations by deleting VEGFR1/FLT1  a VEGFA decoy receptor.  We find that  following cryoinjury  zebrafish flt1 mutant hearts display enhanced coronary revascularization and endocardial expansion  increased cardiomyocyte dedifferentiation and proliferation  and decreased scarring.  Suppressing Vegfa signaling in flt1 mutants abrogates the beneficial effects of flt1 deletion.  Transcriptomic analyses of cryoinjured flt1 mutant hearts revealed enhanced endothelial MAPK/ERK signaling and downregulation of the transcription factor gene egr3.  Using genetic tools  we observe egr3 upregulation in the regenerating endocardium and find that Egr3 promotes myofibroblast differentiation.  These data suggest that with enhanced VEGFA bioavailability  the cardiac endothelium limits myofibroblast differentiation via egr3 downregulation  thereby providing a more permissive microenvironment for cardiomyocyte xxx post injury. Overall design: Comparative gene expression analysis between cryoinjured wild type zebrafish ventricles and flt1 mutant ventricles at 96 hours post cryoinjury.", null, "pubmed:39612288", null, "wild type heart  96 hours post cryoinjury 1", "GSM8217702", null, "source name:heart ventricle border z1 and injured area|tissue:heart ventricle border z1 and injured area|genotype:wild type|treatment:cardiac cryoinjury|geo loc name:missing|collection date:missing", "wild type heart  96 hours post cryoinjury 1", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Aligned reads were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.36.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: danRer11 Supplementary files format and content: library size normlized count matrix", "heart ventricle border zone and injured area", null, "A pool of 5 ventricles was used per biological replicate. Total RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase Free DNase Set  Qiagen 4\u00b5g of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture\u2019s protocol Vazyme.", null, "tissue:heart ventricle border z1 and injured area|genotype:wild type|treatment:cardiac cryoinjury", "GSM8217702", "GSM8217702: wild type heart  96 hours post cryoinjury 1; Danio rerio; RNA Seq", "GSM8217702 r1", "GSM8217702", "1", "A pool of 5 ventricles was used per biological replicate. Total RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase Free DNase Set  Qiagen 4\u00b5g of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture's protocol Vazyme.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP502845", null, "loader:fastq load.py", "E23_4173_Armaad_Lib_WT1_R1.fastq.gz", "fastq", 3571478400.0, 52133215.0, "GSM8217702 r1", "0:68.51", "A:928171678;C:814216251;G:835024543;T:992630615;N:1435313", 68, null, null, null, 928171678, 814216251, 835024543, 992630615, 1435313, "SRX24311223", "SRS21073228", "SRA1849558", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.94111, null, 0.08647, null, 0.72922, null, 0.50812, null, 42, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-04-19", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [31899, "SRR28745435", "SRX24311222", "SRS21073226", "SRP502845", "PRJNA1102356", "flt1 inactivation promotes zebrafish cardiac regeneration by enhancing endothelial activity and limiting the fibrotic response", "GSE264406", "Transcriptome Analysis", "VEGFA administration has been explored as a pro angiogenic therapy for cardiovascular diseases including heart failure for several years; however  many challenges remain.  Here we investigate a different approach to augmenting VEGFA bioavailability  one that achieves more physiological VEGFA concentrations by deleting VEGFR1/FLT1  a VEGFA decoy receptor.  We find that  following cryoinjury  zebrafish flt1 mutant hearts display enhanced coronary revascularization and endocardial expansion  increased cardiomyocyte dedifferentiation and proliferation  and decreased scarring.  Suppressing Vegfa signaling in flt1 mutants abrogates the beneficial effects of flt1 deletion.  Transcriptomic analyses of cryoinjured flt1 mutant hearts revealed enhanced endothelial MAPK/ERK signaling and downregulation of the transcription factor gene egr3.  Using genetic tools  we observe egr3 upregulation in the regenerating endocardium and find that Egr3 promotes myofibroblast differentiation.  These data suggest that with enhanced VEGFA bioavailability  the cardiac endothelium limits myofibroblast differentiation via egr3 downregulation  thereby providing a more permissive microenvironment for cardiomyocyte xxx post injury. Overall design: Comparative gene expression analysis between cryoinjured wild type zebrafish ventricles and flt1 mutant ventricles at 96 hours post cryoinjury.", null, "pubmed:39612288", null, "flt1 mutant heart  96 hours post cryoinjury 3", "GSM8217701", null, "source name:heart ventricle border z1 and injured area|tissue:heart ventricle border z1 and injured area|genotype:flt1bns29/bns29|treatment:cardiac cryoinjury|geo loc name:missing|collection date:missing", "flt1 mutant heart  96 hours post cryoinjury 3", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Aligned reads were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.36.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: danRer11 Supplementary files format and content: library size normlized count matrix", "heart ventricle border zone and injured area", null, "A pool of 5 ventricles was used per biological replicate. Total RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase Free DNase Set  Qiagen 4\u00b5g of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture\u2019s protocol Vazyme.", null, "tissue:heart ventricle border z1 and injured area|genotype:flt1bns29/bns29|treatment:cardiac cryoinjury", "GSM8217701", "GSM8217701: flt1 mutant heart  96 hours post cryoinjury 3; Danio rerio; RNA Seq", "GSM8217701 r1", "GSM8217701", "1", "A pool of 5 ventricles was used per biological replicate. Total RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase Free DNase Set  Qiagen 4\u00b5g of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture's protocol Vazyme.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP502845", null, "loader:fastq load.py", "E23_4173_Armaad_Lib_FLT_MUT3_R1.fastq.gz", "fastq", 4085359270.0, 59673604.0, "GSM8217701 r1", "0:68.46", "A:1050667797;C:938174838;G:953989485;T:1140941596;N:1585554", 68, null, null, null, 1050667797, 938174838, 953989485, 1140941596, 1585554, "SRX24311222", "SRS21073226", "SRA1849558", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.94035, null, 0.08631, null, 0.72376, null, 0.49828, null, 69, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-04-19", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [31900, "SRR28745436", "SRX24311221", "SRS21073225", "SRP502845", "PRJNA1102356", "flt1 inactivation promotes zebrafish cardiac regeneration by enhancing endothelial activity and limiting the fibrotic response", "GSE264406", "Transcriptome Analysis", "VEGFA administration has been explored as a pro angiogenic therapy for cardiovascular diseases including heart failure for several years; however  many challenges remain.  Here we investigate a different approach to augmenting VEGFA bioavailability  one that achieves more physiological VEGFA concentrations by deleting VEGFR1/FLT1  a VEGFA decoy receptor.  We find that  following cryoinjury  zebrafish flt1 mutant hearts display enhanced coronary revascularization and endocardial expansion  increased cardiomyocyte dedifferentiation and proliferation  and decreased scarring.  Suppressing Vegfa signaling in flt1 mutants abrogates the beneficial effects of flt1 deletion.  Transcriptomic analyses of cryoinjured flt1 mutant hearts revealed enhanced endothelial MAPK/ERK signaling and downregulation of the transcription factor gene egr3.  Using genetic tools  we observe egr3 upregulation in the regenerating endocardium and find that Egr3 promotes myofibroblast differentiation.  These data suggest that with enhanced VEGFA bioavailability  the cardiac endothelium limits myofibroblast differentiation via egr3 downregulation  thereby providing a more permissive microenvironment for cardiomyocyte xxx post injury. Overall design: Comparative gene expression analysis between cryoinjured wild type zebrafish ventricles and flt1 mutant ventricles at 96 hours post cryoinjury.", null, "pubmed:39612288", null, "flt1 mutant heart  96 hours post cryoinjury 2", "GSM8217700", null, "source name:heart ventricle border z1 and injured area|tissue:heart ventricle border z1 and injured area|genotype:flt1bns29/bns29|treatment:cardiac cryoinjury|geo loc name:missing|collection date:missing", "flt1 mutant heart  96 hours post cryoinjury 2", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Aligned reads were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.36.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: danRer11 Supplementary files format and content: library size normlized count matrix", "heart ventricle border zone and injured area", null, "A pool of 5 ventricles was used per biological replicate. Total RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase Free DNase Set  Qiagen 4\u00b5g of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture\u2019s protocol Vazyme.", null, "tissue:heart ventricle border z1 and injured area|genotype:flt1bns29/bns29|treatment:cardiac cryoinjury", "GSM8217700", "GSM8217700: flt1 mutant heart  96 hours post cryoinjury 2; Danio rerio; RNA Seq", "GSM8217700 r1", "GSM8217700", "1", "A pool of 5 ventricles was used per biological replicate. Total RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase Free DNase Set  Qiagen 4\u00b5g of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture's protocol Vazyme.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP502845", null, "loader:fastq load.py", "E23_4173_Armaad_Lib_FLT_MUT2_R1.fastq.gz", "fastq", 4696922408.0, 68645737.0, "GSM8217700 r1", "0:68.42", "A:1220019708;C:1072448104;G:1106194472;T:1296618556;N:1641568", 68, null, null, null, 1220019708, 1072448104, 1106194472, 1296618556, 1641568, "SRX24311221", "SRS21073225", "SRA1849558", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.94205, null, 0.08792, null, 0.72543, null, 0.50566, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-04-19", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [31901, "SRR28745437", "SRX24311220", "SRS21073224", "SRP502845", "PRJNA1102356", "flt1 inactivation promotes zebrafish cardiac regeneration by enhancing endothelial activity and limiting the fibrotic response", "GSE264406", "Transcriptome Analysis", "VEGFA administration has been explored as a pro angiogenic therapy for cardiovascular diseases including heart failure for several years; however  many challenges remain.  Here we investigate a different approach to augmenting VEGFA bioavailability  one that achieves more physiological VEGFA concentrations by deleting VEGFR1/FLT1  a VEGFA decoy receptor.  We find that  following cryoinjury  zebrafish flt1 mutant hearts display enhanced coronary revascularization and endocardial expansion  increased cardiomyocyte dedifferentiation and proliferation  and decreased scarring.  Suppressing Vegfa signaling in flt1 mutants abrogates the beneficial effects of flt1 deletion.  Transcriptomic analyses of cryoinjured flt1 mutant hearts revealed enhanced endothelial MAPK/ERK signaling and downregulation of the transcription factor gene egr3.  Using genetic tools  we observe egr3 upregulation in the regenerating endocardium and find that Egr3 promotes myofibroblast differentiation.  These data suggest that with enhanced VEGFA bioavailability  the cardiac endothelium limits myofibroblast differentiation via egr3 downregulation  thereby providing a more permissive microenvironment for cardiomyocyte xxx post injury. Overall design: Comparative gene expression analysis between cryoinjured wild type zebrafish ventricles and flt1 mutant ventricles at 96 hours post cryoinjury.", null, "pubmed:39612288", null, "flt1 mutant heart  96 hours post cryoinjury 1", "GSM8217699", null, "source name:heart ventricle border z1 and injured area|tissue:heart ventricle border z1 and injured area|genotype:flt1bns29/bns29|treatment:cardiac cryoinjury|geo loc name:missing|collection date:missing", "flt1 mutant heart  96 hours post cryoinjury 1", "Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides Bolger et al.  Trimmomatic: a flexible trimmer for Illumina sequence data. Reads were aligned versus Ensembl zebrafish genome version danRer11 Ensembl release 104 with STAR 2.7.10a Aligned reads were filtered to remove: duplicates with Picard 3.0.0 Picard: A set of tools in Java for working with next generation sequencing data in the BAM format  multi mapping  ribosomal  or mitochondrial reads. Gene counts were established with featureCounts 2.0.4 by aggregating reads overlapping exons excluding those overlapping multiple genes Liao et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. The raw count matrix was normalized with DESeq2 version 1.36.0 Love et al.  Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5  multiple testing adjusted p value < 0.05  and  0.585 < log2FC > 0.585. The Ensemble annotation was enriched with UniProt data Activities at the Universal Protein Resource UniProt. Assembly: danRer11 Supplementary files format and content: library size normlized count matrix", "heart ventricle border zone and injured area", null, "A pool of 5 ventricles was used per biological replicate. Total RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase Free DNase Set  Qiagen 4\u00b5g of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture\u2019s protocol Vazyme.", null, "tissue:heart ventricle border z1 and injured area|genotype:flt1bns29/bns29|treatment:cardiac cryoinjury", "GSM8217699", "GSM8217699: flt1 mutant heart  96 hours post cryoinjury 1; Danio rerio; RNA Seq", "GSM8217699 r1", "GSM8217699", "1", "A pool of 5 ventricles was used per biological replicate. Total RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion RNase Free DNase Set  Qiagen 4\u00b5g of total RNA was used as input for VAHTS Stranded mRNA seq V6 Library preparation following manufacture's protocol Vazyme.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 2000", null, "SRP502845", null, "loader:fastq load.py", "E23_4173_Armaad_Lib_FLT_MUT1_R1.fastq.gz", "fastq", 2897934017.0, 42657803.0, "GSM8217699 r1", "0:67.93", "A:749045495;C:662930035;G:683478060;T:800853726;N:1626701", 67, null, null, null, 749045495, 662930035, 683478060, 800853726, 1626701, "SRX24311220", "SRS21073224", "SRA1849558", "MPI for heart and lung research", "MPI for heart and lung research", 1, 0.94107, null, 0.08304, null, 0.72579, null, 0.50482, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-04-19", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [37255, "SRR1043688", "SRX387598", "SRS511498", "SRP033532", "PRJNA230686", "Expression profiling in the heart of wild type and kctd10 mutant zebrafish larvae", "GSE53022", "Transcriptome Analysis", "We sequenced mRNA of hearts from 50 wild type and 50 kctd10 mutant embryos at 48 hpf. Overall design: Examination of mRNA levels in the larvae hearts between the the wt and the kctd10 mutant.", null, "pubmed:24430697", null, "kctd10 mut zebrafish heart", "GSM1280516", null, "source name:heart|strain background:AB|development stage:48 hpf|genotype/variation:kctd10  /  kctd10 mutant|tissue:heart", "kctd10 mut zebrafish heart", "sequenced by the Illumina Hiseq 2000 platform Around 200 million 50 bp single end reads were obtained per sample. Reads were aligned to zebrafish genome Zv9 using tophat  with up to 2 mismatches allowed. Differential expression analysis was performed using DESeq. Genome build: zebrafish genome Zv9 Supplementary files format and content: excel file of relative gene expression level between the wt and the kctd10 mutant. Supplementary files format and content: tab delimited txt files of gene raw counts and DESeq processed relative gene expression level between the wt and the kctd10 mutant.", "heart", null, "Total RNAs from wild type and kctd10 mutant fish hearts were isolated with RNeasy Mini Kit Qiagen  purified with RNeasy columns QIAGEN. Next generation sequencing libraries were prepared with the Illumina TruSeq preparation kit Illumina according to manufacturer's protocol", null, "strain background:AB|development stage:48 hpf|genotype/variation:kctd10  /  kctd10 mutant|tissue:heart", "GSM1280516", "GSM1280516: kctd10 mut zebrafish heart; Danio rerio; RNA Seq", "GSM1280516", null, "1", "Total RNAs from wild type and kctd10 mutant fish hearts were isolated with RNeasy Mini Kit Qiagen  purified with RNeasy columns QIAGEN. Next generation sequencing libraries were prepared with the Illumina TruSeq preparation kit Illumina according to manufacturer's protocol", "GEO Accession:GSM1280516", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP033532", null, null, "s_8_1_1101_qseq.txt.gz", "Illumina native", 159161750.0, 3183235.0, "GSM1280516 r1", "0:50", "A:40560849;C:38239286;G:38051715;T:41572492;N:737408", 50, null, null, null, 40560849, 38239286, 38051715, 41572492, 737408, "SRX387598", "SRS511498", "SRA115339", "GEO", "College of Life Sciences, Peking University", 1, 0.93678, null, 0.06225, null, 0.68834, null, 0.44699, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2013-12-05", "Hatching", "Embryo", "Heart", "Cardiovascular System"], [37256, "SRR1104059", "SRX387598", "SRS511498", "SRP033532", "PRJNA230686", "Expression profiling in the heart of wild type and kctd10 mutant zebrafish larvae", "GSE53022", "Transcriptome Analysis", "We sequenced mRNA of hearts from 50 wild type and 50 kctd10 mutant embryos at 48 hpf. Overall design: Examination of mRNA levels in the larvae hearts between the the wt and the kctd10 mutant.", null, "pubmed:24430697", null, "kctd10 mut zebrafish heart", "GSM1280516", null, "source name:heart|strain background:AB|development stage:48 hpf|genotype/variation:kctd10  /  kctd10 mutant|tissue:heart", "kctd10 mut zebrafish heart", "sequenced by the Illumina Hiseq 2000 platform Around 200 million 50 bp single end reads were obtained per sample. Reads were aligned to zebrafish genome Zv9 using tophat  with up to 2 mismatches allowed. Differential expression analysis was performed using DESeq. Genome build: zebrafish genome Zv9 Supplementary files format and content: excel file of relative gene expression level between the wt and the kctd10 mutant. Supplementary files format and content: tab delimited txt files of gene raw counts and DESeq processed relative gene expression level between the wt and the kctd10 mutant.", "heart", null, "Total RNAs from wild type and kctd10 mutant fish hearts were isolated with RNeasy Mini Kit Qiagen  purified with RNeasy columns QIAGEN. Next generation sequencing libraries were prepared with the Illumina TruSeq preparation kit Illumina according to manufacturer's protocol", null, "strain background:AB|development stage:48 hpf|genotype/variation:kctd10  /  kctd10 mutant|tissue:heart", "GSM1280516", "GSM1280516: kctd10 mut zebrafish heart; Danio rerio; RNA Seq", "GSM1280516", null, "1", "Total RNAs from wild type and kctd10 mutant fish hearts were isolated with RNeasy Mini Kit Qiagen  purified with RNeasy columns QIAGEN. Next generation sequencing libraries were prepared with the Illumina TruSeq preparation kit Illumina according to manufacturer's protocol", "GEO Accession:GSM1280516", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP033532", null, null, null, null, 10053590150.0, 201071803.0, "GSM1280516 r2", "0:50", "A:2588651143;C:2370219438;G:2396055158;T:2650913003;N:47751408", 50, null, null, null, 2588651143, 2370219438, 2396055158, 2650913003, 47751408, "SRX387598", "SRS511498", "SRA115339", "GEO", "College of Life Sciences, Peking University", 1, 0.92227, null, 0.06457, null, 0.69367, null, 0.45203, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2013-12-05", "Hatching", "Embryo", "Heart", "Cardiovascular System"], [37257, "SRR1043687", "SRX387597", "SRS511497", "SRP033532", "PRJNA230686", "Expression profiling in the heart of wild type and kctd10 mutant zebrafish larvae", "GSE53022", "Transcriptome Analysis", "We sequenced mRNA of hearts from 50 wild type and 50 kctd10 mutant embryos at 48 hpf. Overall design: Examination of mRNA levels in the larvae hearts between the the wt and the kctd10 mutant.", null, "pubmed:24430697", null, "wt zebrafish heart", "GSM1280515", null, "source name:heart|strain background:AB|development stage:48 hpf|genotype/variation:wt wild type|tissue:heart", "wt zebrafish heart", "sequenced by the Illumina Hiseq 2000 platform Around 200 million 50 bp single end reads were obtained per sample. Reads were aligned to zebrafish genome Zv9 using tophat  with up to 2 mismatches allowed. Differential expression analysis was performed using DESeq. Genome build: zebrafish genome Zv9 Supplementary files format and content: excel file of relative gene expression level between the wt and the kctd10 mutant. Supplementary files format and content: tab delimited txt files of gene raw counts and DESeq processed relative gene expression level between the wt and the kctd10 mutant.", "heart", null, "Total RNAs from wild type and kctd10 mutant fish hearts were isolated with RNeasy Mini Kit Qiagen  purified with RNeasy columns QIAGEN. Next generation sequencing libraries were prepared with the Illumina TruSeq preparation kit Illumina according to manufacturer's protocol", null, "strain background:AB|development stage:48 hpf|genotype/variation:wt wild type|tissue:heart", "GSM1280515", "GSM1280515: wt zebrafish heart; Danio rerio; RNA Seq", "GSM1280515", null, "1", "Total RNAs from wild type and kctd10 mutant fish hearts were isolated with RNeasy Mini Kit Qiagen  purified with RNeasy columns QIAGEN. Next generation sequencing libraries were prepared with the Illumina TruSeq preparation kit Illumina according to manufacturer's protocol", "GEO Accession:GSM1280515", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP033532", null, null, "s_6_1_1101_qseq.txt.gz", "Illumina native", 155968450.0, 3119369.0, "GSM1280515 r1", "0:50", "A:40015379;C:37108086;G:37319547;T:41209982;N:315456", 50, null, null, null, 40015379, 37108086, 37319547, 41209982, 315456, "SRX387597", "SRS511497", "SRA115339", "GEO", "College of Life Sciences, Peking University", 1, 0.92288, null, 0.06296, null, 0.69209, null, 0.4533, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2013-12-05", "Hatching", "Embryo", "Heart", "Cardiovascular System"], [37258, "SRR1104058", "SRX387597", "SRS511497", "SRP033532", "PRJNA230686", "Expression profiling in the heart of wild type and kctd10 mutant zebrafish larvae", "GSE53022", "Transcriptome Analysis", "We sequenced mRNA of hearts from 50 wild type and 50 kctd10 mutant embryos at 48 hpf. Overall design: Examination of mRNA levels in the larvae hearts between the the wt and the kctd10 mutant.", null, "pubmed:24430697", null, "wt zebrafish heart", "GSM1280515", null, "source name:heart|strain background:AB|development stage:48 hpf|genotype/variation:wt wild type|tissue:heart", "wt zebrafish heart", "sequenced by the Illumina Hiseq 2000 platform Around 200 million 50 bp single end reads were obtained per sample. Reads were aligned to zebrafish genome Zv9 using tophat  with up to 2 mismatches allowed. Differential expression analysis was performed using DESeq. Genome build: zebrafish genome Zv9 Supplementary files format and content: excel file of relative gene expression level between the wt and the kctd10 mutant. Supplementary files format and content: tab delimited txt files of gene raw counts and DESeq processed relative gene expression level between the wt and the kctd10 mutant.", "heart", null, "Total RNAs from wild type and kctd10 mutant fish hearts were isolated with RNeasy Mini Kit Qiagen  purified with RNeasy columns QIAGEN. Next generation sequencing libraries were prepared with the Illumina TruSeq preparation kit Illumina according to manufacturer's protocol", null, "strain background:AB|development stage:48 hpf|genotype/variation:wt wild type|tissue:heart", "GSM1280515", "GSM1280515: wt zebrafish heart; Danio rerio; RNA Seq", "GSM1280515", null, "1", "Total RNAs from wild type and kctd10 mutant fish hearts were isolated with RNeasy Mini Kit Qiagen  purified with RNeasy columns QIAGEN. Next generation sequencing libraries were prepared with the Illumina TruSeq preparation kit Illumina according to manufacturer's protocol", "GEO Accession:GSM1280515", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP033532", null, null, null, null, 10404769750.0, 208095395.0, "GSM1280515 r2", "0:50", "A:2661715782;C:2489013308;G:2484808257;T:2727159333;N:42073070", 50, null, null, null, 2661715782, 2489013308, 2484808257, 2727159333, 42073070, "SRX387597", "SRS511497", "SRA115339", "GEO", "College of Life Sciences, Peking University", 1, 0.93515, null, 0.0656, null, 0.68986, null, 0.45312, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2013-12-05", "Hatching", "Embryo", "Heart", "Cardiovascular System"], [37923, "SRR1554489", "SRX685394", "SRS686642", "SRP039502", "PRJNA240316", "Danio rerio strain:AB Transcriptome or Gene expression", "PRJNA240316", "Transcriptome Analysis", "Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.", null, "pubmed:24835514", null, null, "ZF2Heart1", null, "strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97408|sex:male|tissue:Heart|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Zebrafish Heart2", "ZF2Heart2", "1", "Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3\u2019 adenylated adapter that ligates onto miRs and other small RNAs with a 3\u2019 hydroxyl group.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP039502", null, null, "ZF2_Heart_3.fq.gz", "fastq", 1302765670.0, 12898670.0, "Heart2 Run3", "0:101", "A:397689061;C:312745449;G:268626802;T:323141419;N:562939", 101, null, null, null, 397689061, 312745449, 268626802, 323141419, 562939, "SRX685394", "SRS686642", "SRA142461", "University of Oregon|JHP-Lab", "University of Oregon", 1, 3e-05, null, 2e-05, null, 0.99997, null, 1.0, null, 101, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2014-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [37927, "SRR1554477", "SRX685389", "SRS566618", "SRP039502", "PRJNA240316", "Danio rerio strain:AB Transcriptome or Gene expression", "PRJNA240316", "Transcriptome Analysis", "Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.", null, "pubmed:24835514", null, null, "ZF1Heart1", null, "strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97404|sex:male|tissue:Heart|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Zebrafish individual 1 heart", "ZF1Heart2", "1", "Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3\u2019 adenylated adapter that ligates onto miRs and other small RNAs with a 3\u2019 hydroxyl group.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>101</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP039502", null, null, "ZF1_Heart_3.fq.gz", "fastq", 1561371524.0, 15459124.0, "Heart1 Run3", "0:101", "A:454757966;C:391143691;G:334715236;T:380114024;N:640607", 101, null, null, null, 454757966, 391143691, 334715236, 380114024, 640607, "SRX685389", "SRS566618", "SRA142461", "University of Oregon|JHP-Lab", "University of Oregon", 1, 3e-05, null, 2e-05, null, 0.99997, null, 1.0, null, 101, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2014-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [37933, "SRR1554487", "SRX683351", "SRS686642", "SRP039502", "PRJNA240316", "Danio rerio strain:AB Transcriptome or Gene expression", "PRJNA240316", "Transcriptome Analysis", "Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.", null, "pubmed:24835514", null, null, "ZF2Heart1", null, "strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97408|sex:male|tissue:Heart|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Zebrafish Heart2", "ZF2Heart1", "1", "Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3\u2019 adenylated adapter that ligates onto miRs and other small RNAs with a 3\u2019 hydroxyl group.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP039502", null, null, "ZF2_Heart_1.fq.gz", "fastq", 767836212.0, 15055612.0, "Heart2 Run1", "0:51", "A:192620363;C:202013249;G:191038597;T:181862075;N:301928", 51, null, null, null, 192620363, 202013249, 191038597, 181862075, 301928, "SRX683351", "SRS686642", "SRA142461", "University of Oregon|JHP-Lab", "University of Oregon", 1, 5e-05, null, 3e-05, null, 0.99995, null, 1.0, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2014-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [37934, "SRR1554488", "SRX683351", "SRS686642", "SRP039502", "PRJNA240316", "Danio rerio strain:AB Transcriptome or Gene expression", "PRJNA240316", "Transcriptome Analysis", "Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.", null, "pubmed:24835514", null, null, "ZF2Heart1", null, "strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97408|sex:male|tissue:Heart|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Zebrafish Heart2", "ZF2Heart1", "1", "Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3\u2019 adenylated adapter that ligates onto miRs and other small RNAs with a 3\u2019 hydroxyl group.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP039502", null, null, "ZF2_Heart_2.fq.gz", "fastq", 979886205.0, 19213455.0, "Heart2 Run2", "0:51", "A:246169086;C:264387065;G:236377487;T:227289693;N:5662874", 51, null, null, null, 246169086, 264387065, 236377487, 227289693, 5662874, "SRX683351", "SRS686642", "SRA142461", "University of Oregon|JHP-Lab", "University of Oregon", 1, 2e-05, null, 0.0, null, 1.0, null, null, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2014-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [37941, "SRR1554475", "SRX482035", "SRS566618", "SRP039502", "PRJNA240316", "Danio rerio strain:AB Transcriptome or Gene expression", "PRJNA240316", "Transcriptome Analysis", "Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.", null, "pubmed:24835514", null, null, "ZF1Heart1", null, "strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97404|sex:male|tissue:Heart|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Zebrafish individual 1 heart", "ZF1Heart1", "1", "Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3\u2019 adenylated adapter that ligates onto miRs and other small RNAs with a 3\u2019 hydroxyl group.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP039502", null, null, "ZF1_Heart_1.fq.gz", "fastq", 810162642.0, 15885542.0, "Heart1 Run1", "0:51", "A:199665102;C:213941735;G:204361738;T:191870055;N:324012", 51, null, null, null, 199665102, 213941735, 204361738, 191870055, 324012, "SRX482035", "SRS566618", "SRA142461", "University of Oregon|JHP-Lab", "University of Oregon", 1, 6e-05, null, 1e-05, null, 0.99989, null, 0.8, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2014-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [37942, "SRR1554476", "SRX482035", "SRS566618", "SRP039502", "PRJNA240316", "Danio rerio strain:AB Transcriptome or Gene expression", "PRJNA240316", "Transcriptome Analysis", "Quantifying expression levels of smallRNAs between tissues in Danio Rerio strain AB.", null, "pubmed:24835514", null, null, "ZF1Heart1", null, "strain:AB|age:Reproductive Adult|biomaterial provider:Postlethwait Lab Institute of Neuroscience 1254 University of Oregon 222 Huestis Hall Eugene OR  97404|sex:male|tissue:Heart|birth location:University of Oregon Fish Facility|collected by:Thomas Desvignes|collection date:2013 10 07|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Zebrafish individual 1 heart", "ZF1Heart1", "1", "Tissue specific sequencing libraries were prepped and barcoded using the BiooScientific NEXTflex smallRNA Sequencing Kit  which uses a 3\u2019 adenylated adapter that ligates onto miRs and other small RNAs with a 3\u2019 hydroxyl group.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>51</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP039502", null, null, "ZF1_Heart_2.fq.gz", "fastq", 1013563698.0, 19873798.0, "Heart1 Run2", "0:51", "A:249913434;C:275453651;G:247166233;T:235034199;N:5996181", 51, null, null, null, 249913434, 275453651, 247166233, 235034199, 5996181, "SRX482035", "SRS566618", "SRA142461", "University of Oregon|JHP-Lab", "University of Oregon", 1, 4e-05, null, 2e-05, null, 0.99997, null, 0.0, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2014-08-22", "Adult", "Adult", "Heart", "Cardiovascular System"], [37991, "SRR1265766", "SRX529160", "SRS598857", "SRP041544", "PRJNA245824", "Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish", "GSE57169", "Transcriptome Analysis", "The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish  substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain  gut  liver  ovary  testis  eye  heart and embryo of zebrafish.  In brain  gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs  with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2  we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0%  with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs  respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further  we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as  a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling  novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.", null, "pubmed:26574018", null, "Heart Replicate 3 sRNAseq", "GSM1376649", null, "source name:Heart|tissue:Heart|genetic background:Wild type   Singapore strain", "Heart Replicate 3 sRNAseq", "Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedl\u00e4nder et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database  finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl  p <zebrafish precursor miRNA fasta file>  m <zebrafish mature miRNA fasta file>  r <unique reads fasta file>  t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.", "Heart", "N/A", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560  Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the  mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using  TruSeq Small RNA Sample Preparation Kit  RS 200 0012  Illumina  Inc.. Libraries were prepared according to manufacturer instructions. Briefly  1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "Fishes were purchased from a local supplier and acclimatized before tissue extraction.", "tissue:Heart|genetic background:Wild type   Singapore strain", "GSM1376649", "GSM1376649: Heart Replicate 3 sRNAseq; Danio rerio; miRNA Seq", "GSM1376649", null, "1", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560  Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the  mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using  TruSeq Small RNA Sample Preparation Kit  RS 200 0012  Illumina  Inc.. Libraries were prepared according to manufacturer instructions. Briefly  1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "GEO Accession:GSM1376649", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP041544", null, null, "MZH008_GATCAG_L005_R1.fastq.gz", "fastq", 4401229692.0, 57910917.0, "GSM1376649 r1", "0:76", "A:1009381958;C:1130057881;G:1173217392;T:1088123982;N:448479", 76, null, null, null, 1009381958, 1130057881, 1173217392, 1088123982, 448479, "SRX529160", "SRS598857", "SRA160430", "GEO", "Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore", 1, 0.00129, null, 0.00046, null, 0.99882, null, 0.51351, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Singapore", "2014-04-29", "Undetermined", "Embryo", "Heart", "Cardiovascular System"], [37992, "SRR1265765", "SRX529159", "SRS598856", "SRP041544", "PRJNA245824", "Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish", "GSE57169", "Transcriptome Analysis", "The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish  substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain  gut  liver  ovary  testis  eye  heart and embryo of zebrafish.  In brain  gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs  with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2  we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0%  with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs  respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further  we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as  a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling  novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.", null, "pubmed:26574018", null, "Heart Replicate 2 sRNAseq", "GSM1376648", null, "source name:Heart|tissue:Heart|genetic background:Wild type   Singapore strain", "Heart Replicate 2 sRNAseq", "Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedl\u00e4nder et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database  finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl  p <zebrafish precursor miRNA fasta file>  m <zebrafish mature miRNA fasta file>  r <unique reads fasta file>  t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.", "Heart", "N/A", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560  Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the  mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using  TruSeq Small RNA Sample Preparation Kit  RS 200 0012  Illumina  Inc.. Libraries were prepared according to manufacturer instructions. Briefly  1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "Fishes were purchased from a local supplier and acclimatized before tissue extraction.", "tissue:Heart|genetic background:Wild type   Singapore strain", "GSM1376648", "GSM1376648: Heart Replicate 2 sRNAseq; Danio rerio; miRNA Seq", "GSM1376648", null, "1", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560  Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the  mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using  TruSeq Small RNA Sample Preparation Kit  RS 200 0012  Illumina  Inc.. Libraries were prepared according to manufacturer instructions. Briefly  1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "GEO Accession:GSM1376648", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP041544", null, null, "MZH007_ACTTGA_L005_R1.fastq.gz", "fastq", 3202357508.0, 42136283.0, "GSM1376648 r1", "0:76", "A:666309720;C:845347679;G:846066601;T:844306103;N:327405", 76, null, null, null, 666309720, 845347679, 846066601, 844306103, 327405, "SRX529159", "SRS598856", "SRA160430", "GEO", "Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore", 1, 0.00042, null, 3e-05, null, 0.99924, null, 0.56521, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Singapore", "2014-04-29", "Undetermined", "Embryo", "Heart", "Cardiovascular System"], [37993, "SRR1265764", "SRX529158", "SRS598855", "SRP041544", "PRJNA245824", "Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish", "GSE57169", "Transcriptome Analysis", "The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish  substantially less microRNAs have been discovered in zebrafish compared to human Release 19. It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain  gut  liver  ovary  testis  eye  heart and embryo of zebrafish.  In brain  gut and liver sequencing was done in male and female separately. Majority of the sequenced reads 16 62% mapped to known miRNAs  with the exception of ovary 5.7% and testis 7.8%. Using the miRNA discovery tool miRDeep2  we discovered novel miRNAs from the un annotated reads that ranged from 7.6 to 23.0%  with exceptions of ovary 51.4% and testis 55.2%. The prediction tool identified a total of 459 novel pre miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated 22 and sex associated 34 miRNAs  respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further  we have discovered 459 novel pre miRNAs 30% seed homology to human miRNA as  a genomic resource which can facilitate further investigations to understand miRNA mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Overall design: Known miRNA profiling  novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish in triplicate was carried out using the Illumina HiSeq 2000 platform.", null, "pubmed:26574018", null, "Heart Replicate 1 sRNAseq", "GSM1376647", null, "source name:Heart|tissue:Heart|genetic background:Wild type   Singapore strain", "Heart Replicate 1 sRNAseq", "Illumina Casava 1.8.2 software used for basecalling. The sequenced reads were first subjected to adapter removal through the cutadapt program Martin 2011. The trimmed reads were then collapsed to remove redundancy and to obtain a unique sequence fasta file through the mapper module of miRDeep2 package Friedl\u00e4nder et al. 2012. The unique reads fasta file was then put through an elimination pipeline module Vaz et al. 2010 comprising of a series of sequence similarity searches with the annotated databases. At each step the reads were matched to an annotated database with a maximum of two mismatches. The matched reads were removed and the unmatched ones were further matched to another annotated database  finally culminating into an un annotated pool of reads that served as a source of novel miRNAs and novel sRNAs. The known miRNA expression profile was generated by using the quantifier module of the miRDeep2 package that gives the read counts for the known miRNAs. The quantifier.pl command line used: perl quantifier.pl  p <zebrafish precursor miRNA fasta file>  m <zebrafish mature miRNA fasta file>  r <unique reads fasta file>  t Zebrafish The raw reads expression profile generated for all the replicates of the samples were subjected to Trimmed Mean of M values TMM normalisation using the Bioconductor package edgeR Robinson et al. 2010. Genome build: ZV9 Supplementary files format and content: 1. 'Danio rerio known miRNA Rel19 profile Raw.txt': Tab delimited text file that includes the raw counts for the known mature miRNA miRBase Release 19. Supplementary files format and content: 2. 'Danio rerio known miRNA Rel19 profile Normalised.txt': Tab delimited text file that includes the Trimmed Mean of M values TMM normalised counts for the known mature miRNA miRBase Release 19. One of the replicate of Heart MZH008 failed to cluster with the other two replicates on basis of its known miRNA expression profile and hence was not used for further analysis.", "Heart", "N/A", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560  Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the  mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using  TruSeq Small RNA Sample Preparation Kit  RS 200 0012  Illumina  Inc.. Libraries were prepared according to manufacturer instructions. Briefly  1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "Fishes were purchased from a local supplier and acclimatized before tissue extraction.", "tissue:Heart|genetic background:Wild type   Singapore strain", "GSM1376647", "GSM1376647: Heart Replicate 1 sRNAseq; Danio rerio; miRNA Seq", "GSM1376647", null, "1", "Total RNA were extracted using mirVana\u2122 miRNA Isolation Kit AM1560  Life Technologies. Tissues were homogenised in 1.5 ml microfuge tube containing Lysis/Binding buffer provided in the  mirVana\u2122 miRNA Isolation using a hand held pestle. Total RNA containing small RNA were purified following the manufacturer protocol. Small RNA libraries were prepared for sequencing using  TruSeq Small RNA Sample Preparation Kit  RS 200 0012  Illumina  Inc.. Libraries were prepared according to manufacturer instructions. Briefly  1\u00b5g of good quality Total RNA per sample was used as starting material. 5\u2019 and 3\u2019 RNA adapters were ligated to each RNA molecule before reverse transcription to create single stranded cDNA. The cDNA was then amplified with PCR using a common primer and a primer containing a unique index sequence. The resulting PCR reactions were electrophoresed on 6% Novex TBE PAGE Gel Life Technologies and bands corresponding to adapter ligated constructs derived from 22 30 nucleotides small RNA fragments were excised from the gel. The small RNA were purified from the excised gel and validated on High Sensitivity DNA chips on a Bioanalyser Agilent Technologies before sequencing.", "GEO Accession:GSM1376647", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP041544", null, null, "MZH002_CAGATC_L005_R1.fastq.gz", "fastq", 3777814232.0, 49708082.0, "GSM1376647 r1", "0:76", "A:791204432;C:1050679958;G:1001897360;T:933655799;N:376683", 76, null, null, null, 791204432, 1050679958, 1001897360, 933655799, 376683, "SRX529158", "SRS598855", "SRA160430", "GEO", "Expression and Signaling in Mesenchymal and Hematopoietic Stem Cells, Genome and Gene Expression Data Analysis Division, Bioinformatics Institute, A*STAR, Singapore", 1, 0.00034, null, 4e-05, null, 0.99943, null, 0.62264, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Singapore", "2014-04-29", "Undetermined", "Embryo", "Heart", "Cardiovascular System"], [39650, "SRR2013392", "SRX1021209", "SRS931170", "SRP058095", "PRJNA283297", "Injury activated endocardium plays structural and signalling roles in zebrafish heart regeneration", "GSE68650", "Transcriptome Analysis", "The zebrafish heart remarkably regenerates post a severe ventricular damage followed by inflammation  fibrotic tissue deposition and removal concomitant with cardiac muscle replacement. We have investigated the role of the endocardium in this regeneration process. 3D whole mount imaging in injured hearts revealed that GFP labelled endocardial cells in ET33mi 60A transgenic fish become rapidly activated and highly proliferative at 3 days post cryoinjury dpci. Endocardial cells extensively expand within the injury site and organize to form a coherent structure at 9 dpci that persists throughout the regeneration process. Upon injury  endocardial cells strongly up regulate the Notch pathway ligand delta like4 dll4 and the Notch receptors notch1b  notch2 and notch3. Expression profiling showed that Notch signalling inhibition affects endocardial gene expression and genes related to extracellular matrix remodelling and inflammation. Gain  and loss of function experiments revealed that Notch is required for the organization of the endocardium  attenuation of the inflammatory response and cardiomyocyte proliferation. These results demonstrate a novel structural and signalling role for the endocardium during heart regeneration. Overall design: RNA was extracted from apical tip of heart ventricles 72h post cryoinjured adult zebrafish heart treated with DMSO Controls or RO gamma secretase inhibitor at 24 and xxx post injury.", null, "pubmed:28242613", null, "RO Treated 4", "GSM1678062", null, "source name:apex of 3 hearts|developmental stage:adult|strain:AB|stress:cryoinjury|treatment:RO gamma secretase inhibitor|tissue:Heart", "RO Treated 4", "Illumina RTA software v 1.13.48.0 Fastq files extracted with CASAVA 1.8 Reads were pre processed with Cutadapt 1.6.1  To remove TruSeq adaptor. Resulting reads were mapped on the zebrafish transcriptome Ensembl gene build GRCZv9.v75; ftp://ftp.ensembl.org/pub/release 75/gtf/danio rerio/Danio rerio.Zv9.75.gtf.gz and gene expression quantified using RSEM v1.2.3 and Bowtie2 v2.0.6. Data were normalized using TMM with the Bioconductor package EdgeR Differential expression were tested using GLM with the Bioconductor package EdgeR Genome build: GRCZv9.v75 Supplementary files format and content: ROvsControl.NormCounts.csv reports TMM normalized counts per million reads sequenced", "apex of 3 hearts", "Adult fish were injected with peritoneal RO or DMSO carrier 24h and 48h post cryoinjury of the heart", "Total RNA was extracted using Trizol Invitrogen And then purified on Rneasy spin columns Qiagen. RNA integrity RNA Integrity Score \u2265 7.9 And quantity were determined on the Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using TruSeq RNA Sample Preparation Kit v2 standard Illumina protocols", "Standard protocols were used to maintain the zebrafish to maturity", "developmental stage:adult|strain:AB|stress:cryoinjury|treatment:RO gamma secretase inhibitor|tissue:Heart", "GSM1678062", "GSM1678062: RO Treated 4; Danio rerio; RNA Seq", "GSM1678062", null, "1", "Total RNA was extracted using Trizol Invitrogen And then purified on Rneasy spin columns Qiagen. RNA integrity RNA Integrity Score \u2265 7.9 And quantity were determined on the Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using TruSeq RNA Sample Preparation Kit v2 standard Illumina protocols", "GEO Accession:GSM1678062", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP058095", null, null, "RO4__JulianeMunch_RNASeq_ACTTGA_L003_R1_001.fastq.gz", "fastq", 427948875.0, 5705985.0, "GSM1678062 r1", "0:75", "A:115814965;C:99544699;G:96761732;T:115801235;N:26244", 75, null, null, null, 115814965, 99544699, 96761732, 115801235, 26244, "SRX1021209", "SRS931170", "SRA266952", "GEO", "Intercellular Signalling in Cardiovascular Development & Disease, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC).", 1, 0.92416, null, 0.09021, null, 0.73801, null, 0.5064, null, 75, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Spain", "2015-05-07", "Adult", "Adult", "Heart", "Cardiovascular System"], [39651, "SRR2013391", "SRX1021208", "SRS931171", "SRP058095", "PRJNA283297", "Injury activated endocardium plays structural and signalling roles in zebrafish heart regeneration", "GSE68650", "Transcriptome Analysis", "The zebrafish heart remarkably regenerates post a severe ventricular damage followed by inflammation  fibrotic tissue deposition and removal concomitant with cardiac muscle replacement. We have investigated the role of the endocardium in this regeneration process. 3D whole mount imaging in injured hearts revealed that GFP labelled endocardial cells in ET33mi 60A transgenic fish become rapidly activated and highly proliferative at 3 days post cryoinjury dpci. Endocardial cells extensively expand within the injury site and organize to form a coherent structure at 9 dpci that persists throughout the regeneration process. Upon injury  endocardial cells strongly up regulate the Notch pathway ligand delta like4 dll4 and the Notch receptors notch1b  notch2 and notch3. Expression profiling showed that Notch signalling inhibition affects endocardial gene expression and genes related to extracellular matrix remodelling and inflammation. Gain  and loss of function experiments revealed that Notch is required for the organization of the endocardium  attenuation of the inflammatory response and cardiomyocyte proliferation. These results demonstrate a novel structural and signalling role for the endocardium during heart regeneration. Overall design: RNA was extracted from apical tip of heart ventricles 72h post cryoinjured adult zebrafish heart treated with DMSO Controls or RO gamma secretase inhibitor at 24 and xxx post injury.", null, "pubmed:28242613", null, "RO Treated 3", "GSM1678061", null, "source name:apex of 3 hearts|developmental stage:adult|strain:AB|stress:cryoinjury|treatment:RO gamma secretase inhibitor|tissue:Heart", "RO Treated 3", "Illumina RTA software v 1.13.48.0 Fastq files extracted with CASAVA 1.8 Reads were pre processed with Cutadapt 1.6.1  To remove TruSeq adaptor. Resulting reads were mapped on the zebrafish transcriptome Ensembl gene build GRCZv9.v75; ftp://ftp.ensembl.org/pub/release 75/gtf/danio rerio/Danio rerio.Zv9.75.gtf.gz and gene expression quantified using RSEM v1.2.3 and Bowtie2 v2.0.6. Data were normalized using TMM with the Bioconductor package EdgeR Differential expression were tested using GLM with the Bioconductor package EdgeR Genome build: GRCZv9.v75 Supplementary files format and content: ROvsControl.NormCounts.csv reports TMM normalized counts per million reads sequenced", "apex of 3 hearts", "Adult fish were injected with peritoneal RO or DMSO carrier 24h and 48h post cryoinjury of the heart", "Total RNA was extracted using Trizol Invitrogen And then purified on Rneasy spin columns Qiagen. RNA integrity RNA Integrity Score \u2265 7.9 And quantity were determined on the Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using TruSeq RNA Sample Preparation Kit v2 standard Illumina protocols", "Standard protocols were used to maintain the zebrafish to maturity", "developmental stage:adult|strain:AB|stress:cryoinjury|treatment:RO gamma secretase inhibitor|tissue:Heart", "GSM1678061", "GSM1678061: RO Treated 3; Danio rerio; RNA Seq", "GSM1678061", null, "1", "Total RNA was extracted using Trizol Invitrogen And then purified on Rneasy spin columns Qiagen. RNA integrity RNA Integrity Score \u2265 7.9 And quantity were determined on the Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using TruSeq RNA Sample Preparation Kit v2 standard Illumina protocols", "GEO Accession:GSM1678061", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP058095", null, null, "RO3__JulianeMunch_RNASeq_CAGATC_L003_R1_001.fastq.gz", "fastq", 455559150.0, 6074122.0, "GSM1678061 r1", "0:75", "A:122363593;C:107125528;G:103884219;T:122157436;N:28374", 75, null, null, null, 122363593, 107125528, 103884219, 122157436, 28374, "SRX1021208", "SRS931171", "SRA266952", "GEO", "Intercellular Signalling in Cardiovascular Development & Disease, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC).", 1, 0.92764, null, 0.08686, null, 0.73712, null, 0.50429, null, 75, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Spain", "2015-05-07", "Adult", "Adult", "Heart", "Cardiovascular System"], [39652, "SRR2013390", "SRX1021207", "SRS931169", "SRP058095", "PRJNA283297", "Injury activated endocardium plays structural and signalling roles in zebrafish heart regeneration", "GSE68650", "Transcriptome Analysis", "The zebrafish heart remarkably regenerates post a severe ventricular damage followed by inflammation  fibrotic tissue deposition and removal concomitant with cardiac muscle replacement. We have investigated the role of the endocardium in this regeneration process. 3D whole mount imaging in injured hearts revealed that GFP labelled endocardial cells in ET33mi 60A transgenic fish become rapidly activated and highly proliferative at 3 days post cryoinjury dpci. Endocardial cells extensively expand within the injury site and organize to form a coherent structure at 9 dpci that persists throughout the regeneration process. Upon injury  endocardial cells strongly up regulate the Notch pathway ligand delta like4 dll4 and the Notch receptors notch1b  notch2 and notch3. Expression profiling showed that Notch signalling inhibition affects endocardial gene expression and genes related to extracellular matrix remodelling and inflammation. Gain  and loss of function experiments revealed that Notch is required for the organization of the endocardium  attenuation of the inflammatory response and cardiomyocyte proliferation. These results demonstrate a novel structural and signalling role for the endocardium during heart regeneration. Overall design: RNA was extracted from apical tip of heart ventricles 72h post cryoinjured adult zebrafish heart treated with DMSO Controls or RO gamma secretase inhibitor at 24 and xxx post injury.", null, "pubmed:28242613", null, "RO Treated 2", "GSM1678060", null, "source name:apex of 3 hearts|developmental stage:adult|strain:AB|stress:cryoinjury|treatment:RO gamma secretase inhibitor|tissue:Heart", "RO Treated 2", "Illumina RTA software v 1.13.48.0 Fastq files extracted with CASAVA 1.8 Reads were pre processed with Cutadapt 1.6.1  To remove TruSeq adaptor. Resulting reads were mapped on the zebrafish transcriptome Ensembl gene build GRCZv9.v75; ftp://ftp.ensembl.org/pub/release 75/gtf/danio rerio/Danio rerio.Zv9.75.gtf.gz and gene expression quantified using RSEM v1.2.3 and Bowtie2 v2.0.6. Data were normalized using TMM with the Bioconductor package EdgeR Differential expression were tested using GLM with the Bioconductor package EdgeR Genome build: GRCZv9.v75 Supplementary files format and content: ROvsControl.NormCounts.csv reports TMM normalized counts per million reads sequenced", "apex of 3 hearts", "Adult fish were injected with peritoneal RO or DMSO carrier 24h and 48h post cryoinjury of the heart", "Total RNA was extracted using Trizol Invitrogen And then purified on Rneasy spin columns Qiagen. RNA integrity RNA Integrity Score \u2265 7.9 And quantity were determined on the Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using TruSeq RNA Sample Preparation Kit v2 standard Illumina protocols", "Standard protocols were used to maintain the zebrafish to maturity", "developmental stage:adult|strain:AB|stress:cryoinjury|treatment:RO gamma secretase inhibitor|tissue:Heart", "GSM1678060", "GSM1678060: RO Treated 2; Danio rerio; RNA Seq", "GSM1678060", null, "1", "Total RNA was extracted using Trizol Invitrogen And then purified on Rneasy spin columns Qiagen. RNA integrity RNA Integrity Score \u2265 7.9 And quantity were determined on the Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using TruSeq RNA Sample Preparation Kit v2 standard Illumina protocols", "GEO Accession:GSM1678060", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP058095", null, null, "RO2__JulianeMunch_RNASeq_GCCAAT_L003_R1_001.fastq.gz", "fastq", 386650200.0, 5155336.0, "GSM1678060 r1", "0:75", "A:104806248;C:90193815;G:87370083;T:104256628;N:23426", 75, null, null, null, 104806248, 90193815, 87370083, 104256628, 23426, "SRX1021207", "SRS931169", "SRA266952", "GEO", "Intercellular Signalling in Cardiovascular Development & Disease, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC).", 1, 0.92706, null, 0.09783, null, 0.73783, null, 0.52738, null, 75, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Spain", "2015-05-07", "Adult", "Adult", "Heart", "Cardiovascular System"], [39653, "SRR2013389", "SRX1021206", "SRS931172", "SRP058095", "PRJNA283297", "Injury activated endocardium plays structural and signalling roles in zebrafish heart regeneration", "GSE68650", "Transcriptome Analysis", "The zebrafish heart remarkably regenerates post a severe ventricular damage followed by inflammation  fibrotic tissue deposition and removal concomitant with cardiac muscle replacement. We have investigated the role of the endocardium in this regeneration process. 3D whole mount imaging in injured hearts revealed that GFP labelled endocardial cells in ET33mi 60A transgenic fish become rapidly activated and highly proliferative at 3 days post cryoinjury dpci. Endocardial cells extensively expand within the injury site and organize to form a coherent structure at 9 dpci that persists throughout the regeneration process. Upon injury  endocardial cells strongly up regulate the Notch pathway ligand delta like4 dll4 and the Notch receptors notch1b  notch2 and notch3. Expression profiling showed that Notch signalling inhibition affects endocardial gene expression and genes related to extracellular matrix remodelling and inflammation. Gain  and loss of function experiments revealed that Notch is required for the organization of the endocardium  attenuation of the inflammatory response and cardiomyocyte proliferation. These results demonstrate a novel structural and signalling role for the endocardium during heart regeneration. Overall design: RNA was extracted from apical tip of heart ventricles 72h post cryoinjured adult zebrafish heart treated with DMSO Controls or RO gamma secretase inhibitor at 24 and xxx post injury.", null, "pubmed:28242613", null, "DMSO Control 3", "GSM1678059", null, "source name:apex of 3 hearts|developmental stage:adult|strain:AB|stress:cryoinjury|treatment:control|tissue:Heart", "DMSO Control 3", "Illumina RTA software v 1.13.48.0 Fastq files extracted with CASAVA 1.8 Reads were pre processed with Cutadapt 1.6.1  To remove TruSeq adaptor. Resulting reads were mapped on the zebrafish transcriptome Ensembl gene build GRCZv9.v75; ftp://ftp.ensembl.org/pub/release 75/gtf/danio rerio/Danio rerio.Zv9.75.gtf.gz and gene expression quantified using RSEM v1.2.3 and Bowtie2 v2.0.6. Data were normalized using TMM with the Bioconductor package EdgeR Differential expression were tested using GLM with the Bioconductor package EdgeR Genome build: GRCZv9.v75 Supplementary files format and content: ROvsControl.NormCounts.csv reports TMM normalized counts per million reads sequenced", "apex of 3 hearts", "Adult fish were injected with peritoneal RO or DMSO carrier 24h and 48h post cryoinjury of the heart", "Total RNA was extracted using Trizol Invitrogen And then purified on Rneasy spin columns Qiagen. RNA integrity RNA Integrity Score \u2265 7.9 And quantity were determined on the Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using TruSeq RNA Sample Preparation Kit v2 standard Illumina protocols", "Standard protocols were used to maintain the zebrafish to maturity", "developmental stage:adult|strain:AB|stress:cryoinjury|treatment:control|tissue:Heart", "GSM1678059", "GSM1678059: DMSO Control 3; Danio rerio; RNA Seq", "GSM1678059", null, "1", "Total RNA was extracted using Trizol Invitrogen And then purified on Rneasy spin columns Qiagen. RNA integrity RNA Integrity Score \u2265 7.9 And quantity were determined on the Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using TruSeq RNA Sample Preparation Kit v2 standard Illumina protocols", "GEO Accession:GSM1678059", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP058095", null, null, "DMSO3__JulianeMunch_RNASeq_TTAGGC_L002_R1_001.fastq.gz", "fastq", 335316600.0, 4470888.0, "GSM1678059 r1", "0:75", "A:90648552;C:77961611;G:75841369;T:90772355;N:92713", 75, null, null, null, 90648552, 77961611, 75841369, 90772355, 92713, "SRX1021206", "SRS931172", "SRA266952", "GEO", "Intercellular Signalling in Cardiovascular Development & Disease, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC).", 1, 0.92509, null, 0.08415, null, 0.73434, null, 0.49782, null, 75, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Spain", "2015-05-07", "Adult", "Adult", "Heart", "Cardiovascular System"], [39654, "SRR2013388", "SRX1021205", "SRS931173", "SRP058095", "PRJNA283297", "Injury activated endocardium plays structural and signalling roles in zebrafish heart regeneration", "GSE68650", "Transcriptome Analysis", "The zebrafish heart remarkably regenerates post a severe ventricular damage followed by inflammation  fibrotic tissue deposition and removal concomitant with cardiac muscle replacement. We have investigated the role of the endocardium in this regeneration process. 3D whole mount imaging in injured hearts revealed that GFP labelled endocardial cells in ET33mi 60A transgenic fish become rapidly activated and highly proliferative at 3 days post cryoinjury dpci. Endocardial cells extensively expand within the injury site and organize to form a coherent structure at 9 dpci that persists throughout the regeneration process. Upon injury  endocardial cells strongly up regulate the Notch pathway ligand delta like4 dll4 and the Notch receptors notch1b  notch2 and notch3. Expression profiling showed that Notch signalling inhibition affects endocardial gene expression and genes related to extracellular matrix remodelling and inflammation. Gain  and loss of function experiments revealed that Notch is required for the organization of the endocardium  attenuation of the inflammatory response and cardiomyocyte proliferation. These results demonstrate a novel structural and signalling role for the endocardium during heart regeneration. Overall design: RNA was extracted from apical tip of heart ventricles 72h post cryoinjured adult zebrafish heart treated with DMSO Controls or RO gamma secretase inhibitor at 24 and xxx post injury.", null, "pubmed:28242613", null, "DMSO Control 2", "GSM1678058", null, "source name:apex of 3 hearts|developmental stage:adult|strain:AB|stress:cryoinjury|treatment:control|tissue:Heart", "DMSO Control 2", "Illumina RTA software v 1.13.48.0 Fastq files extracted with CASAVA 1.8 Reads were pre processed with Cutadapt 1.6.1  To remove TruSeq adaptor. Resulting reads were mapped on the zebrafish transcriptome Ensembl gene build GRCZv9.v75; ftp://ftp.ensembl.org/pub/release 75/gtf/danio rerio/Danio rerio.Zv9.75.gtf.gz and gene expression quantified using RSEM v1.2.3 and Bowtie2 v2.0.6. Data were normalized using TMM with the Bioconductor package EdgeR Differential expression were tested using GLM with the Bioconductor package EdgeR Genome build: GRCZv9.v75 Supplementary files format and content: ROvsControl.NormCounts.csv reports TMM normalized counts per million reads sequenced", "apex of 3 hearts", "Adult fish were injected with peritoneal RO or DMSO carrier 24h and 48h post cryoinjury of the heart", "Total RNA was extracted using Trizol Invitrogen And then purified on Rneasy spin columns Qiagen. RNA integrity RNA Integrity Score \u2265 7.9 And quantity were determined on the Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using TruSeq RNA Sample Preparation Kit v2 standard Illumina protocols", "Standard protocols were used to maintain the zebrafish to maturity", "developmental stage:adult|strain:AB|stress:cryoinjury|treatment:control|tissue:Heart", "GSM1678058", "GSM1678058: DMSO Control 2; Danio rerio; RNA Seq", "GSM1678058", null, "1", "Total RNA was extracted using Trizol Invitrogen And then purified on Rneasy spin columns Qiagen. RNA integrity RNA Integrity Score \u2265 7.9 And quantity were determined on the Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using TruSeq RNA Sample Preparation Kit v2 standard Illumina protocols", "GEO Accession:GSM1678058", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP058095", null, null, "DMSO2__JulianeMunch_RNASeq_CGATGT_L002_R1_001.fastq.gz", "fastq", 414318450.0, 5524246.0, "GSM1678058 r1", "0:75", "A:112160824;C:96305097;G:93445540;T:112291936;N:115053", 75, null, null, null, 112160824, 96305097, 93445540, 112291936, 115053, "SRX1021205", "SRS931173", "SRA266952", "GEO", "Intercellular Signalling in Cardiovascular Development & Disease, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC).", 1, 0.92455, null, 0.09161, null, 0.73841, null, 0.49623, null, 75, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Spain", "2015-05-07", "Adult", "Adult", "Heart", "Cardiovascular System"], [39655, "SRR2013387", "SRX1021204", "SRS931174", "SRP058095", "PRJNA283297", "Injury activated endocardium plays structural and signalling roles in zebrafish heart regeneration", "GSE68650", "Transcriptome Analysis", "The zebrafish heart remarkably regenerates post a severe ventricular damage followed by inflammation  fibrotic tissue deposition and removal concomitant with cardiac muscle replacement. We have investigated the role of the endocardium in this regeneration process. 3D whole mount imaging in injured hearts revealed that GFP labelled endocardial cells in ET33mi 60A transgenic fish become rapidly activated and highly proliferative at 3 days post cryoinjury dpci. Endocardial cells extensively expand within the injury site and organize to form a coherent structure at 9 dpci that persists throughout the regeneration process. Upon injury  endocardial cells strongly up regulate the Notch pathway ligand delta like4 dll4 and the Notch receptors notch1b  notch2 and notch3. Expression profiling showed that Notch signalling inhibition affects endocardial gene expression and genes related to extracellular matrix remodelling and inflammation. Gain  and loss of function experiments revealed that Notch is required for the organization of the endocardium  attenuation of the inflammatory response and cardiomyocyte proliferation. These results demonstrate a novel structural and signalling role for the endocardium during heart regeneration. Overall design: RNA was extracted from apical tip of heart ventricles 72h post cryoinjured adult zebrafish heart treated with DMSO Controls or RO gamma secretase inhibitor at 24 and xxx post injury.", null, "pubmed:28242613", null, "DMSO Control 1", "GSM1678057", null, "source name:apex of 3 hearts|developmental stage:adult|strain:AB|stress:cryoinjury|treatment:control|tissue:Heart", "DMSO Control 1", "Illumina RTA software v 1.13.48.0 Fastq files extracted with CASAVA 1.8 Reads were pre processed with Cutadapt 1.6.1  To remove TruSeq adaptor. Resulting reads were mapped on the zebrafish transcriptome Ensembl gene build GRCZv9.v75; ftp://ftp.ensembl.org/pub/release 75/gtf/danio rerio/Danio rerio.Zv9.75.gtf.gz and gene expression quantified using RSEM v1.2.3 and Bowtie2 v2.0.6. Data were normalized using TMM with the Bioconductor package EdgeR Differential expression were tested using GLM with the Bioconductor package EdgeR Genome build: GRCZv9.v75 Supplementary files format and content: ROvsControl.NormCounts.csv reports TMM normalized counts per million reads sequenced", "apex of 3 hearts", "Adult fish were injected with peritoneal RO or DMSO carrier 24h and 48h post cryoinjury of the heart", "Total RNA was extracted using Trizol Invitrogen And then purified on Rneasy spin columns Qiagen. RNA integrity RNA Integrity Score \u2265 7.9 And quantity were determined on the Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using TruSeq RNA Sample Preparation Kit v2 standard Illumina protocols", "Standard protocols were used to maintain the zebrafish to maturity", "developmental stage:adult|strain:AB|stress:cryoinjury|treatment:control|tissue:Heart", "GSM1678057", "GSM1678057: DMSO Control 1; Danio rerio; RNA Seq", "GSM1678057", null, "1", "Total RNA was extracted using Trizol Invitrogen And then purified on Rneasy spin columns Qiagen. RNA integrity RNA Integrity Score \u2265 7.9 And quantity were determined on the Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using TruSeq RNA Sample Preparation Kit v2 standard Illumina protocols", "GEO Accession:GSM1678057", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP058095", null, null, "DMSO1__JulianeMunch_RNASeq_ATCACG_L002_R1_001.fastq.gz", "fastq", 422642625.0, 5635235.0, "GSM1678057 r1", "0:75", "A:115397920;C:98566641;G:95338915;T:113221724;N:117425", 75, null, null, null, 115397920, 98566641, 95338915, 113221724, 117425, "SRX1021204", "SRS931174", "SRA266952", "GEO", "Intercellular Signalling in Cardiovascular Development & Disease, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC).", 1, 0.92302, null, 0.08485, null, 0.73377, null, 0.50474, null, 75, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Spain", "2015-05-07", "Adult", "Adult", "Heart", "Cardiovascular System"], [39801, "SRR2146373", "SRX1134132", "SRS1024030", "SRP062067", "PRJNA292013", "Telomerase is essential for zebrafish heart regeneration", "GSE71755", "Transcriptome Analysis", "Unlike human hearts  zebrafish hearts efficiently xxx post injury. Regeneration is driven by the strong proliferation response of its cardiomyocytes to injury. In this study  we show that active telomerase is required for cardiomyocyte proliferation and full organ recovery  supporting the potential of telomerase therapy as a means of stimulating cell proliferation upon myocardial infarction. Overall design: Heart transcriptomes of WT and telomerase defective adult zebrafish animals were profiled by RNASeq  in control conditions and 3 days post heart cryoinjury.", null, "pubmed:26321646", null, "WT Cryoinjury 4", "GSM1844648", null, "source name:Heart|genotype/variation:WT|stress:cryoinjury|time:3 days post cryoinjury|tissue:heart", "WT Cryoinjury 4", "Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3. Genome build: Zv9 Ensembl gene build 66 Supplementary files format and content: matrix table.txt contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.", "Heart", null, "Four biological replicates consisting of 3 pooled hearts were used per sample. Index tagged cDNA libraries were constructed from total RNA 1 \u03bcg with the TruSeq RNA Sample Preparation v2 Kit Illumina  San Diego  CA.", "All experiments were conducted with adult zebrafish between 6 month and 9 month of age  raised at a density of 3 fish/l.", "genotype/variation:WT|stress:cryoinjury|time:3 days post cryoinjury|tissue:heart", "GSM1844648", "GSM1844648: WT Cryoinjury 4; Danio rerio; RNA Seq", "GSM1844648", null, "1", "Four biological replicates consisting of 3 pooled hearts were used per sample. Index tagged cDNA libraries were constructed from total RNA 1 \u03bcg with the TruSeq RNA Sample Preparation v2 Kit Illumina  San Diego  CA.", "GEO Accession:GSM1844648", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP062067", null, null, "R34_WI4_ACTTGA_L003_R1_001.fastq.gz", "fastq", 1180343100.0, 19672385.0, "GSM1844648 r1", "0:60", "A:319842922;C:273116749;G:267948507;T:319217594;N:217328", 60, null, null, null, 319842922, 273116749, 267948507, 319217594, 217328, "SRX1134132", "SRS1024030", "SRA282285", "GEO", "Bioinformatics Unit, CNIC", 1, 0.926, null, 0.08416, null, 0.74016, null, 0.4997, null, 60, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Spain", "2015-08-05", "Adult", "Adult", "Heart", "Cardiovascular System"], [39802, "SRR2146372", "SRX1134131", "SRS1024031", "SRP062067", "PRJNA292013", "Telomerase is essential for zebrafish heart regeneration", "GSE71755", "Transcriptome Analysis", "Unlike human hearts  zebrafish hearts efficiently xxx post injury. Regeneration is driven by the strong proliferation response of its cardiomyocytes to injury. In this study  we show that active telomerase is required for cardiomyocyte proliferation and full organ recovery  supporting the potential of telomerase therapy as a means of stimulating cell proliferation upon myocardial infarction. Overall design: Heart transcriptomes of WT and telomerase defective adult zebrafish animals were profiled by RNASeq  in control conditions and 3 days post heart cryoinjury.", null, "pubmed:26321646", null, "WT Cryoinjury 3", "GSM1844647", null, "source name:Heart|genotype/variation:WT|stress:cryoinjury|time:3 days post cryoinjury|tissue:heart", "WT Cryoinjury 3", "Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3. Genome build: Zv9 Ensembl gene build 66 Supplementary files format and content: matrix table.txt contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.", "Heart", null, "Four biological replicates consisting of 3 pooled hearts were used per sample. Index tagged cDNA libraries were constructed from total RNA 1 \u03bcg with the TruSeq RNA Sample Preparation v2 Kit Illumina  San Diego  CA.", "All experiments were conducted with adult zebrafish between 6 month and 9 month of age  raised at a density of 3 fish/l.", "genotype/variation:WT|stress:cryoinjury|time:3 days post cryoinjury|tissue:heart", "GSM1844647", "GSM1844647: WT Cryoinjury 3; Danio rerio; RNA Seq", "GSM1844647", null, "1", "Four biological replicates consisting of 3 pooled hearts were used per sample. Index tagged cDNA libraries were constructed from total RNA 1 \u03bcg with the TruSeq RNA Sample Preparation v2 Kit Illumina  San Diego  CA.", "GEO Accession:GSM1844647", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP062067", null, null, "R34_WI3_CAGATC_L002_R1_001.fastq.gz", "fastq", 720538380.0, 12008973.0, "GSM1844647 r1", "0:60", "A:198422177;C:163859167;G:160659168;T:197464680;N:133188", 60, null, null, null, 198422177, 163859167, 160659168, 197464680, 133188, "SRX1134131", "SRS1024031", "SRA282285", "GEO", "Bioinformatics Unit, CNIC", 1, 0.92633, null, 0.09695, null, 0.73965, null, 0.49466, null, 60, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Spain", "2015-08-05", "Adult", "Adult", "Heart", "Cardiovascular System"], [39803, "SRR2146371", "SRX1134130", "SRS1024032", "SRP062067", "PRJNA292013", "Telomerase is essential for zebrafish heart regeneration", "GSE71755", "Transcriptome Analysis", "Unlike human hearts  zebrafish hearts efficiently xxx post injury. Regeneration is driven by the strong proliferation response of its cardiomyocytes to injury. In this study  we show that active telomerase is required for cardiomyocyte proliferation and full organ recovery  supporting the potential of telomerase therapy as a means of stimulating cell proliferation upon myocardial infarction. Overall design: Heart transcriptomes of WT and telomerase defective adult zebrafish animals were profiled by RNASeq  in control conditions and 3 days post heart cryoinjury.", null, "pubmed:26321646", null, "WT Cryoinjury 2", "GSM1844646", null, "source name:Heart|genotype/variation:WT|stress:cryoinjury|time:3 days post cryoinjury|tissue:heart", "WT Cryoinjury 2", "Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3. Genome build: Zv9 Ensembl gene build 66 Supplementary files format and content: matrix table.txt contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.", "Heart", null, "Four biological replicates consisting of 3 pooled hearts were used per sample. Index tagged cDNA libraries were constructed from total RNA 1 \u03bcg with the TruSeq RNA Sample Preparation v2 Kit Illumina  San Diego  CA.", "All experiments were conducted with adult zebrafish between 6 month and 9 month of age  raised at a density of 3 fish/l.", "genotype/variation:WT|stress:cryoinjury|time:3 days post cryoinjury|tissue:heart", "GSM1844646", "GSM1844646: WT Cryoinjury 2; Danio rerio; RNA Seq", "GSM1844646", null, "1", "Four biological replicates consisting of 3 pooled hearts were used per sample. Index tagged cDNA libraries were constructed from total RNA 1 \u03bcg with the TruSeq RNA Sample Preparation v2 Kit Illumina  San Diego  CA.", "GEO Accession:GSM1844646", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP062067", null, null, "R34_WI2_GCCAAT_L001_R1_001.fastq.gz", "fastq", 730971300.0, 12182855.0, "GSM1844646 r1", "0:60", "A:201729903;C:165658242;G:163450866;T:199997922;N:134367", 60, null, null, null, 201729903, 165658242, 163450866, 199997922, 134367, "SRX1134130", "SRS1024032", "SRA282285", "GEO", "Bioinformatics Unit, CNIC", 1, 0.9242, null, 0.09147, null, 0.73829, null, 0.50313, null, 60, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Spain", "2015-08-05", "Adult", "Adult", "Heart", "Cardiovascular System"], [39804, "SRR2146370", "SRX1134129", "SRS1024033", "SRP062067", "PRJNA292013", "Telomerase is essential for zebrafish heart regeneration", "GSE71755", "Transcriptome Analysis", "Unlike human hearts  zebrafish hearts efficiently xxx post injury. Regeneration is driven by the strong proliferation response of its cardiomyocytes to injury. In this study  we show that active telomerase is required for cardiomyocyte proliferation and full organ recovery  supporting the potential of telomerase therapy as a means of stimulating cell proliferation upon myocardial infarction. Overall design: Heart transcriptomes of WT and telomerase defective adult zebrafish animals were profiled by RNASeq  in control conditions and 3 days post heart cryoinjury.", null, "pubmed:26321646", null, "WT Cryoinjury 1", "GSM1844645", null, "source name:Heart|genotype/variation:WT|stress:cryoinjury|time:3 days post cryoinjury|tissue:heart", "WT Cryoinjury 1", "Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3. Genome build: Zv9 Ensembl gene build 66 Supplementary files format and content: matrix table.txt contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.", "Heart", null, "Four biological replicates consisting of 3 pooled hearts were used per sample. Index tagged cDNA libraries were constructed from total RNA 1 \u03bcg with the TruSeq RNA Sample Preparation v2 Kit Illumina  San Diego  CA.", "All experiments were conducted with adult zebrafish between 6 month and 9 month of age  raised at a density of 3 fish/l.", "genotype/variation:WT|stress:cryoinjury|time:3 days post cryoinjury|tissue:heart", "GSM1844645", "GSM1844645: WT Cryoinjury 1; Danio rerio; RNA Seq", "GSM1844645", null, "1", "Four biological replicates consisting of 3 pooled hearts were used per sample. Index tagged cDNA libraries were constructed from total RNA 1 \u03bcg with the TruSeq RNA Sample Preparation v2 Kit Illumina  San Diego  CA.", "GEO Accession:GSM1844645", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP062067", null, null, "R34_WI1_ACAGTG_L001_R1_001.fastq.gz", "fastq", 594823080.0, 9913718.0, "GSM1844645 r1", "0:60", "A:164046346;C:135362608;G:132698406;T:162605589;N:110131", 60, null, null, null, 164046346, 135362608, 132698406, 162605589, 110131, "SRX1134129", "SRS1024033", "SRA282285", "GEO", "Bioinformatics Unit, CNIC", 1, 0.92413, null, 0.09483, null, 0.73714, null, 0.49028, null, 60, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Spain", "2015-08-05", "Adult", "Adult", "Heart", "Cardiovascular System"], [39805, "SRR2146369", "SRX1134128", "SRS1024036", "SRP062067", "PRJNA292013", "Telomerase is essential for zebrafish heart regeneration", "GSE71755", "Transcriptome Analysis", "Unlike human hearts  zebrafish hearts efficiently xxx post injury. Regeneration is driven by the strong proliferation response of its cardiomyocytes to injury. In this study  we show that active telomerase is required for cardiomyocyte proliferation and full organ recovery  supporting the potential of telomerase therapy as a means of stimulating cell proliferation upon myocardial infarction. Overall design: Heart transcriptomes of WT and telomerase defective adult zebrafish animals were profiled by RNASeq  in control conditions and 3 days post heart cryoinjury.", null, "pubmed:26321646", null, "WT Ctrl 4", "GSM1844644", null, "source name:Heart|genotype/variation:WT|stress:Control|tissue:heart", "WT Ctrl 4", "Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3. Genome build: Zv9 Ensembl gene build 66 Supplementary files format and content: matrix table.txt contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.", "Heart", null, "Four biological replicates consisting of 3 pooled hearts were used per sample. Index tagged cDNA libraries were constructed from total RNA 1 \u03bcg with the TruSeq RNA Sample Preparation v2 Kit Illumina  San Diego  CA.", "All experiments were conducted with adult zebrafish between 6 month and 9 month of age  raised at a density of 3 fish/l.", "genotype/variation:WT|stress:Control|tissue:heart", "GSM1844644", "GSM1844644: WT Ctrl 4; Danio rerio; RNA Seq", "GSM1844644", null, "1", "Four biological replicates consisting of 3 pooled hearts were used per sample. 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Regeneration is driven by the strong proliferation response of its cardiomyocytes to injury. In this study  we show that active telomerase is required for cardiomyocyte proliferation and full organ recovery  supporting the potential of telomerase therapy as a means of stimulating cell proliferation upon myocardial infarction. Overall design: Heart transcriptomes of WT and telomerase defective adult zebrafish animals were profiled by RNASeq  in control conditions and 3 days post heart cryoinjury.", null, "pubmed:26321646", null, "WT Ctrl 3", "GSM1844643", null, "source name:Heart|genotype/variation:WT|stress:Control|tissue:heart", "WT Ctrl 3", "Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3. Genome build: Zv9 Ensembl gene build 66 Supplementary files format and content: matrix table.txt contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.", "Heart", null, "Four biological replicates consisting of 3 pooled hearts were used per sample. Index tagged cDNA libraries were constructed from total RNA 1 \u03bcg with the TruSeq RNA Sample Preparation v2 Kit Illumina  San Diego  CA.", "All experiments were conducted with adult zebrafish between 6 month and 9 month of age  raised at a density of 3 fish/l.", "genotype/variation:WT|stress:Control|tissue:heart", "GSM1844643", "GSM1844643: WT Ctrl 3; Danio rerio; RNA Seq", "GSM1844643", null, "1", "Four biological replicates consisting of 3 pooled hearts were used per sample. Index tagged cDNA libraries were constructed from total RNA 1 \u03bcg with the TruSeq RNA Sample Preparation v2 Kit Illumina  San Diego  CA.", "GEO Accession:GSM1844643", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP062067", null, null, "R34_WC3_TTAGGC_L002_R1_001.fastq.gz", "fastq", 716089500.0, 11934825.0, "GSM1844643 r1", "0:60", "A:193750105;C:166517678;G:162185388;T:193504490;N:131839", 60, null, null, null, 193750105, 166517678, 162185388, 193504490, 131839, "SRX1134127", "SRS1024035", "SRA282285", "GEO", "Bioinformatics Unit, CNIC", 1, 0.92529, null, 0.07765, null, 0.77333, null, 0.4841, null, 60, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Spain", "2015-08-05", "Adult", "Adult", "Heart", "Cardiovascular System"], [39807, "SRR2146367", "SRX1134126", "SRS1024034", "SRP062067", "PRJNA292013", "Telomerase is essential for zebrafish heart regeneration", "GSE71755", "Transcriptome Analysis", "Unlike human hearts  zebrafish hearts efficiently xxx post injury. Regeneration is driven by the strong proliferation response of its cardiomyocytes to injury. In this study  we show that active telomerase is required for cardiomyocyte proliferation and full organ recovery  supporting the potential of telomerase therapy as a means of stimulating cell proliferation upon myocardial infarction. Overall design: Heart transcriptomes of WT and telomerase defective adult zebrafish animals were profiled by RNASeq  in control conditions and 3 days post heart cryoinjury.", null, "pubmed:26321646", null, "WT Ctrl 2", "GSM1844642", null, "source name:Heart|genotype/variation:WT|stress:Control|tissue:heart", "WT Ctrl 2", "Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3. Genome build: Zv9 Ensembl gene build 66 Supplementary files format and content: matrix table.txt contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.", "Heart", null, "Four biological replicates consisting of 3 pooled hearts were used per sample. Index tagged cDNA libraries were constructed from total RNA 1 \u03bcg with the TruSeq RNA Sample Preparation v2 Kit Illumina  San Diego  CA.", "All experiments were conducted with adult zebrafish between 6 month and 9 month of age  raised at a density of 3 fish/l.", "genotype/variation:WT|stress:Control|tissue:heart", "GSM1844642", "GSM1844642: WT Ctrl 2; Danio rerio; RNA Seq", "GSM1844642", null, "1", "Four biological replicates consisting of 3 pooled hearts were used per sample. Index tagged cDNA libraries were constructed from total RNA 1 \u03bcg with the TruSeq RNA Sample Preparation v2 Kit Illumina  San Diego  CA.", "GEO Accession:GSM1844642", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP062067", null, null, "R34_WC2_CGATGT_L001_R1_001.fastq.gz", "fastq", 658475520.0, 10974592.0, "GSM1844642 r1", "0:60", "A:181534641;C:149368098;G:146492820;T:180957879;N:122082", 60, null, null, null, 181534641, 149368098, 146492820, 180957879, 122082, "SRX1134126", "SRS1024034", "SRA282285", "GEO", "Bioinformatics Unit, CNIC", 1, 0.92851, null, 0.09073, null, 0.76067, null, 0.49777, null, 60, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Spain", "2015-08-05", "Adult", "Adult", "Heart", "Cardiovascular System"], [39808, "SRR2146366", "SRX1134125", "SRS1024037", "SRP062067", "PRJNA292013", "Telomerase is essential for zebrafish heart regeneration", "GSE71755", "Transcriptome Analysis", "Unlike human hearts  zebrafish hearts efficiently xxx post injury. Regeneration is driven by the strong proliferation response of its cardiomyocytes to injury. In this study  we show that active telomerase is required for cardiomyocyte proliferation and full organ recovery  supporting the potential of telomerase therapy as a means of stimulating cell proliferation upon myocardial infarction. Overall design: Heart transcriptomes of WT and telomerase defective adult zebrafish animals were profiled by RNASeq  in control conditions and 3 days post heart cryoinjury.", null, "pubmed:26321646", null, "WT Ctrl 1", "GSM1844641", null, "source name:Heart|genotype/variation:WT|stress:Control|tissue:heart", "WT Ctrl 1", "Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3. Genome build: Zv9 Ensembl gene build 66 Supplementary files format and content: matrix table.txt contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.", "Heart", null, "Four biological replicates consisting of 3 pooled hearts were used per sample. Index tagged cDNA libraries were constructed from total RNA 1 \u03bcg with the TruSeq RNA Sample Preparation v2 Kit Illumina  San Diego  CA.", "All experiments were conducted with adult zebrafish between 6 month and 9 month of age  raised at a density of 3 fish/l.", "genotype/variation:WT|stress:Control|tissue:heart", "GSM1844641", "GSM1844641: WT Ctrl 1; Danio rerio; RNA Seq", "GSM1844641", null, "1", "Four biological replicates consisting of 3 pooled hearts were used per sample. Index tagged cDNA libraries were constructed from total RNA 1 \u03bcg with the TruSeq RNA Sample Preparation v2 Kit Illumina  San Diego  CA.", "GEO Accession:GSM1844641", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP062067", null, null, "R34_WC1_ATCACG_L001_R1_001.fastq.gz", "fastq", 513876600.0, 8564610.0, "GSM1844641 r1", "0:60", "A:142675384;C:116304684;G:112951733;T:141849640;N:95159", 60, null, null, null, 142675384, 116304684, 112951733, 141849640, 95159, "SRX1134125", "SRS1024037", "SRA282285", "GEO", "Bioinformatics Unit, CNIC", 1, 0.92117, null, 0.09031, null, 0.76715, null, 0.49711, null, 60, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Spain", "2015-08-05", "Adult", "Adult", "Heart", "Cardiovascular System"], [39809, "SRR2146364", "SRX1134124", "SRS1024038", "SRP062067", "PRJNA292013", "Telomerase is essential for zebrafish heart regeneration", "GSE71755", "Transcriptome Analysis", "Unlike human hearts  zebrafish hearts efficiently xxx post injury. Regeneration is driven by the strong proliferation response of its cardiomyocytes to injury. In this study  we show that active telomerase is required for cardiomyocyte proliferation and full organ recovery  supporting the potential of telomerase therapy as a means of stimulating cell proliferation upon myocardial infarction. Overall design: Heart transcriptomes of WT and telomerase defective adult zebrafish animals were profiled by RNASeq  in control conditions and 3 days post heart cryoinjury.", null, "pubmed:26321646", null, "KO Cryoinjury 4", "GSM1844640", null, "source name:Heart|genotype/variation:Tert AB/hu3430 KO mutant|stress:cryoinjury|time:3 days post cryoinjury|tissue:heart", "KO Cryoinjury 4", "Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3. Genome build: Zv9 Ensembl gene build 66 Supplementary files format and content: matrix table.txt contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.", "Heart", null, "Four biological replicates consisting of 3 pooled hearts were used per sample. Index tagged cDNA libraries were constructed from total RNA 1 \u03bcg with the TruSeq RNA Sample Preparation v2 Kit Illumina  San Diego  CA.", "All experiments were conducted with adult zebrafish between 6 month and 9 month of age  raised at a density of 3 fish/l.", "genotype/variation:Tert AB/hu3430 KO mutant|stress:cryoinjury|time:3 days post cryoinjury|tissue:heart", "GSM1844640", "GSM1844640: KO Cryoinjury 4; Danio rerio; RNA Seq", "GSM1844640", null, "1", "Four biological replicates consisting of 3 pooled hearts were used per sample. Index tagged cDNA libraries were constructed from total RNA 1 \u03bcg with the TruSeq RNA Sample Preparation v2 Kit Illumina  San Diego  CA.", "GEO Accession:GSM1844640", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP062067", null, null, "R34_KI4_CCGTCC_L003_R1_001.fastq.gz", "fastq", 311284560.0, 5188076.0, "GSM1844640 r1", "0:60", "A:84154335;C:72206726;G:70916934;T:83949800;N:56765", 60, null, null, null, 84154335, 72206726, 70916934, 83949800, 56765, "SRX1134124", "SRS1024038", "SRA282285", "GEO", "Bioinformatics Unit, CNIC", 1, 0.92625, null, 0.08438, null, 0.74466, null, 0.49683, null, 60, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Spain", "2015-08-05", "Adult", "Adult", "Heart", "Cardiovascular System"], [39810, "SRR2146365", "SRX1134124", "SRS1024038", "SRP062067", "PRJNA292013", "Telomerase is essential for zebrafish heart regeneration", "GSE71755", "Transcriptome Analysis", "Unlike human hearts  zebrafish hearts efficiently xxx post injury. Regeneration is driven by the strong proliferation response of its cardiomyocytes to injury. In this study  we show that active telomerase is required for cardiomyocyte proliferation and full organ recovery  supporting the potential of telomerase therapy as a means of stimulating cell proliferation upon myocardial infarction. Overall design: Heart transcriptomes of WT and telomerase defective adult zebrafish animals were profiled by RNASeq  in control conditions and 3 days post heart cryoinjury.", null, "pubmed:26321646", null, "KO Cryoinjury 4", "GSM1844640", null, "source name:Heart|genotype/variation:Tert AB/hu3430 KO mutant|stress:cryoinjury|time:3 days post cryoinjury|tissue:heart", "KO Cryoinjury 4", "Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3. Genome build: Zv9 Ensembl gene build 66 Supplementary files format and content: matrix table.txt contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.", "Heart", null, "Four biological replicates consisting of 3 pooled hearts were used per sample. Index tagged cDNA libraries were constructed from total RNA 1 \u03bcg with the TruSeq RNA Sample Preparation v2 Kit Illumina  San Diego  CA.", "All experiments were conducted with adult zebrafish between 6 month and 9 month of age  raised at a density of 3 fish/l.", "genotype/variation:Tert AB/hu3430 KO mutant|stress:cryoinjury|time:3 days post cryoinjury|tissue:heart", "GSM1844640", "GSM1844640: KO Cryoinjury 4; Danio rerio; RNA Seq", "GSM1844640", null, "1", "Four biological replicates consisting of 3 pooled hearts were used per sample. Index tagged cDNA libraries were constructed from total RNA 1 \u03bcg with the TruSeq RNA Sample Preparation v2 Kit Illumina  San Diego  CA.", "GEO Accession:GSM1844640", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP062067", null, null, "R35_KI4_CCGTCC_L001_R1_001.fastq.gz", "fastq", 482146575.0, 6428621.0, "GSM1844640 r2", "0:75", "A:130823936;C:111427004;G:109853814;T:129970530;N:71291", 75, null, null, null, 130823936, 111427004, 109853814, 129970530, 71291, "SRX1134124", "SRS1024038", "SRA282285", "GEO", "Bioinformatics Unit, CNIC", 1, 0.92032, null, 0.081, null, 0.74332, null, 0.49429, null, 75, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Spain", "2015-08-05", "Adult", "Adult", "Heart", "Cardiovascular System"], [39811, "SRR2146362", "SRX1134123", "SRS1024040", "SRP062067", "PRJNA292013", "Telomerase is essential for zebrafish heart regeneration", "GSE71755", "Transcriptome Analysis", "Unlike human hearts  zebrafish hearts efficiently xxx post injury. Regeneration is driven by the strong proliferation response of its cardiomyocytes to injury. In this study  we show that active telomerase is required for cardiomyocyte proliferation and full organ recovery  supporting the potential of telomerase therapy as a means of stimulating cell proliferation upon myocardial infarction. Overall design: Heart transcriptomes of WT and telomerase defective adult zebrafish animals were profiled by RNASeq  in control conditions and 3 days post heart cryoinjury.", null, "pubmed:26321646", null, "KO Cryoinjury 3", "GSM1844639", null, "source name:Heart|genotype/variation:Tert AB/hu3430 KO mutant|stress:cryoinjury|time:3 days post cryoinjury|tissue:heart", "KO Cryoinjury 3", "Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3. Genome build: Zv9 Ensembl gene build 66 Supplementary files format and content: matrix table.txt contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.", "Heart", null, "Four biological replicates consisting of 3 pooled hearts were used per sample. Index tagged cDNA libraries were constructed from total RNA 1 \u03bcg with the TruSeq RNA Sample Preparation v2 Kit Illumina  San Diego  CA.", "All experiments were conducted with adult zebrafish between 6 month and 9 month of age  raised at a density of 3 fish/l.", "genotype/variation:Tert AB/hu3430 KO mutant|stress:cryoinjury|time:3 days post cryoinjury|tissue:heart", "GSM1844639", "GSM1844639: KO Cryoinjury 3; Danio rerio; RNA Seq", "GSM1844639", null, "1", "Four biological replicates consisting of 3 pooled hearts were used per sample. Index tagged cDNA libraries were constructed from total RNA 1 \u03bcg with the TruSeq RNA Sample Preparation v2 Kit Illumina  San Diego  CA.", "GEO Accession:GSM1844639", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP062067", null, null, "R34_KI3_ATGTCA_L003_R1_001.fastq.gz", "fastq", 124527660.0, 2075461.0, "GSM1844639 r1", "0:60", "A:33785374;C:28888355;G:28096084;T:33734970;N:22877", 60, null, null, null, 33785374, 28888355, 28096084, 33734970, 22877, "SRX1134123", "SRS1024040", "SRA282285", "GEO", "Bioinformatics Unit, CNIC", 1, 0.92788, null, 0.08408, null, 0.74385, null, 0.50013, null, 60, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Spain", "2015-08-05", "Adult", "Adult", "Heart", "Cardiovascular System"], [39812, "SRR2146363", "SRX1134123", "SRS1024040", "SRP062067", "PRJNA292013", "Telomerase is essential for zebrafish heart regeneration", "GSE71755", "Transcriptome Analysis", "Unlike human hearts  zebrafish hearts efficiently xxx post injury. Regeneration is driven by the strong proliferation response of its cardiomyocytes to injury. In this study  we show that active telomerase is required for cardiomyocyte proliferation and full organ recovery  supporting the potential of telomerase therapy as a means of stimulating cell proliferation upon myocardial infarction. Overall design: Heart transcriptomes of WT and telomerase defective adult zebrafish animals were profiled by RNASeq  in control conditions and 3 days post heart cryoinjury.", null, "pubmed:26321646", null, "KO Cryoinjury 3", "GSM1844639", null, "source name:Heart|genotype/variation:Tert AB/hu3430 KO mutant|stress:cryoinjury|time:3 days post cryoinjury|tissue:heart", "KO Cryoinjury 3", "Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3. Genome build: Zv9 Ensembl gene build 66 Supplementary files format and content: matrix table.txt contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.", "Heart", null, "Four biological replicates consisting of 3 pooled hearts were used per sample. Index tagged cDNA libraries were constructed from total RNA 1 \u03bcg with the TruSeq RNA Sample Preparation v2 Kit Illumina  San Diego  CA.", "All experiments were conducted with adult zebrafish between 6 month and 9 month of age  raised at a density of 3 fish/l.", "genotype/variation:Tert AB/hu3430 KO mutant|stress:cryoinjury|time:3 days post cryoinjury|tissue:heart", "GSM1844639", "GSM1844639: KO Cryoinjury 3; Danio rerio; RNA Seq", "GSM1844639", null, "1", "Four biological replicates consisting of 3 pooled hearts were used per sample. Index tagged cDNA libraries were constructed from total RNA 1 \u03bcg with the TruSeq RNA Sample Preparation v2 Kit Illumina  San Diego  CA.", "GEO Accession:GSM1844639", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP062067", null, null, "R35_KI3_ATGTCA_L001_R1_001.fastq.gz", "fastq", 412690275.0, 5502537.0, "GSM1844639 r2", "0:75", "A:113092589;C:95031274;G:93098999;T:111406088;N:61325", 75, null, null, null, 113092589, 95031274, 93098999, 111406088, 61325, "SRX1134123", "SRS1024040", "SRA282285", "GEO", "Bioinformatics Unit, CNIC", 1, 0.92558, null, 0.08033, null, 0.74669, null, 0.49748, null, 75, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Spain", "2015-08-05", "Adult", "Adult", "Heart", "Cardiovascular System"], [39813, "SRR2146360", "SRX1134122", "SRS1024039", "SRP062067", "PRJNA292013", "Telomerase is essential for zebrafish heart regeneration", "GSE71755", "Transcriptome Analysis", "Unlike human hearts  zebrafish hearts efficiently xxx post injury. Regeneration is driven by the strong proliferation response of its cardiomyocytes to injury. In this study  we show that active telomerase is required for cardiomyocyte proliferation and full organ recovery  supporting the potential of telomerase therapy as a means of stimulating cell proliferation upon myocardial infarction. Overall design: Heart transcriptomes of WT and telomerase defective adult zebrafish animals were profiled by RNASeq  in control conditions and 3 days post heart cryoinjury.", null, "pubmed:26321646", null, "KO Cryoinjury 2", "GSM1844638", null, "source name:Heart|genotype/variation:Tert AB/hu3430 KO mutant|stress:cryoinjury|time:3 days post cryoinjury|tissue:heart", "KO Cryoinjury 2", "Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3. Genome build: Zv9 Ensembl gene build 66 Supplementary files format and content: matrix table.txt contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.", "Heart", null, "Four biological replicates consisting of 3 pooled hearts were used per sample. Index tagged cDNA libraries were constructed from total RNA 1 \u03bcg with the TruSeq RNA Sample Preparation v2 Kit Illumina  San Diego  CA.", "All experiments were conducted with adult zebrafish between 6 month and 9 month of age  raised at a density of 3 fish/l.", "genotype/variation:Tert AB/hu3430 KO mutant|stress:cryoinjury|time:3 days post cryoinjury|tissue:heart", "GSM1844638", "GSM1844638: KO Cryoinjury 2; Danio rerio; RNA Seq", "GSM1844638", null, "1", "Four biological replicates consisting of 3 pooled hearts were used per sample. Index tagged cDNA libraries were constructed from total RNA 1 \u03bcg with the TruSeq RNA Sample Preparation v2 Kit Illumina  San Diego  CA.", "GEO Accession:GSM1844638", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP062067", null, null, "R34_KI2_AGTTCC_L002_R1_001.fastq.gz", "fastq", 96834720.0, 1613912.0, "GSM1844638 r1", "0:60", "A:26359074;C:22287383;G:21837715;T:26332245;N:18303", 60, null, null, null, 26359074, 22287383, 21837715, 26332245, 18303, "SRX1134122", "SRS1024039", "SRA282285", "GEO", "Bioinformatics Unit, CNIC", 1, 0.92622, null, 0.08939, null, 0.73117, null, 0.49207, null, 60, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Spain", "2015-08-05", "Adult", "Adult", "Heart", "Cardiovascular System"], [39814, "SRR2146361", "SRX1134122", "SRS1024039", "SRP062067", "PRJNA292013", "Telomerase is essential for zebrafish heart regeneration", "GSE71755", "Transcriptome Analysis", "Unlike human hearts  zebrafish hearts efficiently xxx post injury. Regeneration is driven by the strong proliferation response of its cardiomyocytes to injury. In this study  we show that active telomerase is required for cardiomyocyte proliferation and full organ recovery  supporting the potential of telomerase therapy as a means of stimulating cell proliferation upon myocardial infarction. Overall design: Heart transcriptomes of WT and telomerase defective adult zebrafish animals were profiled by RNASeq  in control conditions and 3 days post heart cryoinjury.", null, "pubmed:26321646", null, "KO Cryoinjury 2", "GSM1844638", null, "source name:Heart|genotype/variation:Tert AB/hu3430 KO mutant|stress:cryoinjury|time:3 days post cryoinjury|tissue:heart", "KO Cryoinjury 2", "Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3. Genome build: Zv9 Ensembl gene build 66 Supplementary files format and content: matrix table.txt contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.", "Heart", null, "Four biological replicates consisting of 3 pooled hearts were used per sample. Index tagged cDNA libraries were constructed from total RNA 1 \u03bcg with the TruSeq RNA Sample Preparation v2 Kit Illumina  San Diego  CA.", "All experiments were conducted with adult zebrafish between 6 month and 9 month of age  raised at a density of 3 fish/l.", "genotype/variation:Tert AB/hu3430 KO mutant|stress:cryoinjury|time:3 days post cryoinjury|tissue:heart", "GSM1844638", "GSM1844638: KO Cryoinjury 2; Danio rerio; RNA Seq", "GSM1844638", null, "1", "Four biological replicates consisting of 3 pooled hearts were used per sample. Index tagged cDNA libraries were constructed from total RNA 1 \u03bcg with the TruSeq RNA Sample Preparation v2 Kit Illumina  San Diego  CA.", "GEO Accession:GSM1844638", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP062067", null, null, "R35_KI2_AGTTCC_L001_R1_001.fastq.gz", "fastq", 491659200.0, 6555456.0, "GSM1844638 r2", "0:75", "A:133418355;C:113983548;G:111812870;T:132371004;N:73423", 75, null, null, null, 133418355, 113983548, 111812870, 132371004, 73423, "SRX1134122", "SRS1024039", "SRA282285", "GEO", "Bioinformatics Unit, CNIC", 1, 0.91922, null, 0.0824, null, 0.73521, null, 0.49263, null, 75, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "Spain", "2015-08-05", "Adult", "Adult", "Heart", "Cardiovascular System"], [39815, "SRR2146358", "SRX1134121", "SRS1024042", "SRP062067", "PRJNA292013", "Telomerase is essential for zebrafish heart regeneration", "GSE71755", "Transcriptome Analysis", "Unlike human hearts  zebrafish hearts efficiently xxx post injury. Regeneration is driven by the strong proliferation response of its cardiomyocytes to injury. In this study  we show that active telomerase is required for cardiomyocyte proliferation and full organ recovery  supporting the potential of telomerase therapy as a means of stimulating cell proliferation upon myocardial infarction. Overall design: Heart transcriptomes of WT and telomerase defective adult zebrafish animals were profiled by RNASeq  in control conditions and 3 days post heart cryoinjury.", null, "pubmed:26321646", null, "KO Cryoinjury 1", "GSM1844637", null, "source name:Heart|genotype/variation:Tert AB/hu3430 KO mutant|stress:cryoinjury|time:3 days post cryoinjury|tissue:heart", "KO Cryoinjury 1", "Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3. 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