{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Larval\" and tissue_curation = \"Heart\"", "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"], [10216, "ERR6501834", "ERX6129007", "ERS7415871", "ERP131229", "PRJEB46994", "Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf", "E-MTAB-10860", "Transcriptome Analysis", "This experiment sought to understand the transcriptomic changes that occur in the larval zebrafish heart following injury. 600 hearts were laser injured at 3 dpf  extracted 48 hours later and pooled into three groups of 200. RNA was extracted from the whole hearts and sent for sequencing along with 3 groups of 200 uninjured hearts  extracted and processed identically. RNA sequencing  quality control and alignment was performed by the commercial company GENEWIZ.", "ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01", null, "Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 \u03bcg/ml  following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly  30 larvae were placed in 2mL eppendorf tubes  the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4\u00b0C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease  125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 \u03bcg/ml  following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000  the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf", "Uninjured 3", "SAMEA9691614", "University Of Edinburgh", "ENA first public:2021 10 01|ENA last update:2021 10 01|External Id:SAMEA9691614|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 10 01T00:25:01Z|INSDC last update:2021 10 01T00:25:01Z|INSDC status:public|Submitter Id:E MTAB 10860:Uninjured 3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:pool 6 of 200 larvae|organism part:heart|sample name:E MTAB 10860:Uninjured 3|sex:not available|strain:AB", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf", "E MTAB 10860:Uninjured 3 p", "Uninjured 3 p", "Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf", "Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 \u03bcg/ml  following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly  30 larvae were placed in 2mL eppendorf tubes  the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4\u00b0C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease  125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 \u03bcg/ml  following which hearts were extracted.  RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000  the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf", "Experimental Factor: injury:n1", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP131229", "Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf", "ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01", "un-3_R1_001.fastq.gz un-3_R2_001.fastq.gz", "fastq fastq", 18723567013.0, 65061888.0, "E MTAB 10860:un 3 R", "0:143.87 1:143.91", "A:4417527025;C:4932613578;G:4960694819;T:4412305366;N:426225", 143, 143, null, null, 4417527025, 4932613578, 4960694819, 4412305366, 426225, "ERX6129007", "ERS7415871", "ERA5680505", "University Of Edinburgh|European Nucleotide Archive", "University Of Edinburgh|European Nucleotide Archive", 2, 0.96755, 0.96744, 0.18873, 0.18936, 0.72868, 0.73235, 0.632, 0.6437, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United Kingdom", "2021-10-01", "Larval", "Larval", "Heart", "Cardiovascular System"], [10217, "ERR6501833", "ERX6129006", "ERS7415870", "ERP131229", "PRJEB46994", "Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf", "E-MTAB-10860", "Transcriptome Analysis", "This experiment sought to understand the transcriptomic changes that occur in the larval zebrafish heart following injury. 600 hearts were laser injured at 3 dpf  extracted 48 hours later and pooled into three groups of 200. RNA was extracted from the whole hearts and sent for sequencing along with 3 groups of 200 uninjured hearts  extracted and processed identically. RNA sequencing  quality control and alignment was performed by the commercial company GENEWIZ.", "ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01", null, "Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 \u03bcg/ml  following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly  30 larvae were placed in 2mL eppendorf tubes  the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4\u00b0C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease  125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 \u03bcg/ml  following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000  the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf", "Uninjured 2", "SAMEA9691613", "University Of Edinburgh", "ENA first public:2021 10 01|ENA last update:2021 10 01|External Id:SAMEA9691613|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 10 01T00:25:01Z|INSDC last update:2021 10 01T00:25:01Z|INSDC status:public|Submitter Id:E MTAB 10860:Uninjured 2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:pool 5 of 200 larvae|organism part:heart|sample name:E MTAB 10860:Uninjured 2|sex:not available|strain:AB", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf", "E MTAB 10860:Uninjured 2 p", "Uninjured 2 p", "Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf", "Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 \u03bcg/ml  following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly  30 larvae were placed in 2mL eppendorf tubes  the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4\u00b0C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease  125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 \u03bcg/ml  following which hearts were extracted.  RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000  the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf", "Experimental Factor: injury:n1", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP131229", "Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf", "ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01", "un-2_R1_001.fastq.gz un-2_R2_001.fastq.gz", "fastq fastq", 16871358399.0, 59064661.0, "E MTAB 10860:un 2 R", "0:142.77 1:142.88", "A:4041490134;C:4380856328;G:4414614946;T:4033723935;N:673056", 142, 142, null, null, 4041490134, 4380856328, 4414614946, 4033723935, 673056, "ERX6129006", "ERS7415870", "ERA5680505", "University Of Edinburgh|European Nucleotide Archive", "University Of Edinburgh|European Nucleotide Archive", 2, 0.96589, 0.9656, 0.15519, 0.15447, 0.70887, 0.71062, 0.60267, 0.60735, 150, 147, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United Kingdom", "2021-10-01", "Larval", "Larval", "Heart", "Cardiovascular System"], [10218, "ERR6501832", "ERX6129005", "ERS7415869", "ERP131229", "PRJEB46994", "Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf", "E-MTAB-10860", "Transcriptome Analysis", "This experiment sought to understand the transcriptomic changes that occur in the larval zebrafish heart following injury. 600 hearts were laser injured at 3 dpf  extracted 48 hours later and pooled into three groups of 200. RNA was extracted from the whole hearts and sent for sequencing along with 3 groups of 200 uninjured hearts  extracted and processed identically. RNA sequencing  quality control and alignment was performed by the commercial company GENEWIZ.", "ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01", null, "Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 \u03bcg/ml  following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly  30 larvae were placed in 2mL eppendorf tubes  the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4\u00b0C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease  125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 \u03bcg/ml  following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000  the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf", "Uninjured 1", "SAMEA9691612", "University Of Edinburgh", "ENA first public:2021 10 01|ENA last update:2021 10 01|External Id:SAMEA9691612|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 10 01T00:25:01Z|INSDC last update:2021 10 01T00:25:01Z|INSDC status:public|Submitter Id:E MTAB 10860:Uninjured 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:pool 4 of 200 larvae|organism part:heart|sample name:E MTAB 10860:Uninjured 1|sex:not available|strain:AB", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf", "E MTAB 10860:Uninjured 1 p", "Uninjured 1 p", "Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf", "Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 \u03bcg/ml  following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly  30 larvae were placed in 2mL eppendorf tubes  the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4\u00b0C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease  125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 \u03bcg/ml  following which hearts were extracted.  RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000  the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf", "Experimental Factor: injury:n1", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP131229", "Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf", "ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01", "un-1_R1_001.fastq.gz un-1_R2_001.fastq.gz", "fastq fastq", 22029484310.0, 76938931.0, "E MTAB 10860:un 1 R", "0:143.11 1:143.22", "A:5407867825;C:5589867496;G:5636111894;T:5394805343;N:831752", 143, 143, null, null, 5407867825, 5589867496, 5636111894, 5394805343, 831752, "ERX6129005", "ERS7415869", "ERA5680505", "University Of Edinburgh|European Nucleotide Archive", "University Of Edinburgh|European Nucleotide Archive", 2, 0.9602, 0.95957, 0.14282, 0.14408, 0.69649, 0.69954, 0.56712, 0.56916, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United Kingdom", "2021-10-01", "Larval", "Larval", "Heart", "Cardiovascular System"], [10219, "ERR6501831", "ERX6129004", "ERS7415868", "ERP131229", "PRJEB46994", "Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf", "E-MTAB-10860", "Transcriptome Analysis", "This experiment sought to understand the transcriptomic changes that occur in the larval zebrafish heart following injury. 600 hearts were laser injured at 3 dpf  extracted 48 hours later and pooled into three groups of 200. RNA was extracted from the whole hearts and sent for sequencing along with 3 groups of 200 uninjured hearts  extracted and processed identically. RNA sequencing  quality control and alignment was performed by the commercial company GENEWIZ.", "ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01", null, "Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 \u03bcg/ml  following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly  30 larvae were placed in 2mL eppendorf tubes  the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4\u00b0C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease  125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 \u03bcg/ml  following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000  the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf", "Injured 3", "SAMEA9691611", "University Of Edinburgh", "ENA first public:2021 10 01|ENA last update:2021 10 01|External Id:SAMEA9691611|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 10 01T00:25:01Z|INSDC last update:2021 10 01T00:25:01Z|INSDC status:public|Submitter Id:E MTAB 10860:Injured 3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:pool 3 of 200 larvae|organism part:heart|sample name:E MTAB 10860:Injured 3|sex:not available|strain:AB", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf", "E MTAB 10860:Injured 3 p", "Injured 3 p", "Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf", "Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 \u03bcg/ml  following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly  30 larvae were placed in 2mL eppendorf tubes  the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4\u00b0C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease  125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 \u03bcg/ml  following which hearts were extracted.  RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000  the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf", "Experimental Factor: injury:laser injury", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP131229", "Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf", "ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01", "in-3_R1_001.fastq.gz in-3_R2_001.fastq.gz", "fastq fastq", 7393087749.0, 25640713.0, "E MTAB 10860:in 3 R", "0:144.14 1:144.20", "A:1776335117;C:1913125420;G:1928181998;T:1775255039;N:190175", 144, 144, null, null, 1776335117, 1913125420, 1928181998, 1775255039, 190175, "ERX6129004", "ERS7415868", "ERA5680505", "University Of Edinburgh|European Nucleotide Archive", "University Of Edinburgh|European Nucleotide Archive", 2, 0.96032, 0.96001, 0.15921, 0.15882, 0.71417, 0.71869, 0.59876, 0.595, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United Kingdom", "2021-10-01", "Larval", "Larval", "Heart", "Cardiovascular System"], [10220, "ERR6501830", "ERX6129003", "ERS7415867", "ERP131229", "PRJEB46994", "Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf", "E-MTAB-10860", "Transcriptome Analysis", "This experiment sought to understand the transcriptomic changes that occur in the larval zebrafish heart following injury. 600 hearts were laser injured at 3 dpf  extracted 48 hours later and pooled into three groups of 200. RNA was extracted from the whole hearts and sent for sequencing along with 3 groups of 200 uninjured hearts  extracted and processed identically. RNA sequencing  quality control and alignment was performed by the commercial company GENEWIZ.", "ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01", null, "Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 \u03bcg/ml  following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly  30 larvae were placed in 2mL eppendorf tubes  the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4\u00b0C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease  125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 \u03bcg/ml  following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000  the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf", "Injured 2", "SAMEA9691610", "University Of Edinburgh", "ENA first public:2021 10 01|ENA last update:2021 10 01|External Id:SAMEA9691610|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 10 01T00:25:01Z|INSDC last update:2021 10 01T00:25:01Z|INSDC status:public|Submitter Id:E MTAB 10860:Injured 2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:pool 2 of 200 larvae|organism part:heart|sample name:E MTAB 10860:Injured 2|sex:not available|strain:AB", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf", "E MTAB 10860:Injured 2 p", "Injured 2 p", "Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf", "Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 \u03bcg/ml  following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly  30 larvae were placed in 2mL eppendorf tubes  the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4\u00b0C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease  125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 \u03bcg/ml  following which hearts were extracted.  RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000  the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf", "Experimental Factor: injury:laser injury", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP131229", "Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf", "ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01", "in-2_R1_001.fastq.gz in-2_R2_001.fastq.gz", "fastq fastq", 9437508186.0, 33059234.0, "E MTAB 10860:in 2 R", "0:142.70 1:142.77", "A:2291798254;C:2421252733;G:2436117818;T:2288107030;N:232351", 142, 142, null, null, 2291798254, 2421252733, 2436117818, 2288107030, 232351, "ERX6129003", "ERS7415867", "ERA5680505", "University Of Edinburgh|European Nucleotide Archive", "University Of Edinburgh|European Nucleotide Archive", 2, 0.96099, 0.96042, 0.14616, 0.14802, 0.70331, 0.70674, 0.53288, 0.54459, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United Kingdom", "2021-10-01", "Larval", "Larval", "Heart", "Cardiovascular System"], [10221, "ERR6501829", "ERX6129002", "ERS7415866", "ERP131229", "PRJEB46994", "Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf", "E-MTAB-10860", "Transcriptome Analysis", "This experiment sought to understand the transcriptomic changes that occur in the larval zebrafish heart following injury. 600 hearts were laser injured at 3 dpf  extracted 48 hours later and pooled into three groups of 200. RNA was extracted from the whole hearts and sent for sequencing along with 3 groups of 200 uninjured hearts  extracted and processed identically. RNA sequencing  quality control and alignment was performed by the commercial company GENEWIZ.", "ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01", null, "Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 \u03bcg/ml  following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly  30 larvae were placed in 2mL eppendorf tubes  the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4\u00b0C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease  125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 \u03bcg/ml  following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000  the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf", "Injured 1", "SAMEA9691609", "University Of Edinburgh", "ENA first public:2021 10 01|ENA last update:2021 10 01|External Id:SAMEA9691609|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 10 01T00:25:01Z|INSDC last update:2021 10 01T00:25:01Z|INSDC status:public|Submitter Id:E MTAB 10860:Injured 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:pool 1 of 200 larvae|organism part:heart|sample name:E MTAB 10860:Injured 1|sex:not available|strain:AB", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf", "E MTAB 10860:Injured 1 p", "Injured 1 p", "Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf", "Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 \u03bcg/ml  following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly  30 larvae were placed in 2mL eppendorf tubes  the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4\u00b0C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease  125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 \u03bcg/ml  following which hearts were extracted.  RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000  the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf", "Experimental Factor: injury:laser injury", "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP131229", "Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf", "ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01", "in-1_R1_001.fastq.gz in-1_R2_001.fastq.gz", "fastq fastq", 15465552702.0, 54194727.0, "E MTAB 10860:in 1 R", "0:142.59 1:142.78", "A:3807777989;C:3911855097;G:3946385823;T:3798685145;N:848648", 142, 142, null, null, 3807777989, 3911855097, 3946385823, 3798685145, 848648, "ERX6129002", "ERS7415866", "ERA5680505", "University Of Edinburgh|European Nucleotide Archive", "University Of Edinburgh|European Nucleotide Archive", 2, 0.95721, 0.95688, 0.14331, 0.14374, 0.70262, 0.70445, 0.5114, 0.52855, 140, 140, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United Kingdom", "2021-10-01", "Larval", "Larval", "Heart", "Cardiovascular System"], [26482, "SRR25930974", "SRX21649989", "SRS18818461", "SRP458853", "PRJNA1013567", "scRNA seq of 50 hpf and 80 hpf isolated zebrafish hearts", "GSE242483", "Transcriptome Analysis", "Seeking to identify additional transcription factors required for cardiac valve formation  we determined and explored the transcriptional landscape of endocardial cells at the time when key morphogenetic events underlying valve development take place. Overall design: We isolated wild type zebrafish hearts at 50 hpf when valve identity has just been established  and at 80 hpf when forming valves are first observed", null, "pubmed:38748804", null, "80hpf", "GSM7764482", null, "source name:heart|tissue:heart|genotype:wild type|age:80hpf|geo loc name:missing|collection date:missing", "80hpf", "Reads were aligned against the zebrafish genome and counted by StarSolo. Preprocessed counts were further analysed using Scanpy. Basic cell quality control was conducted by taking the number of detected genes and mitochondrial content into consideration. We removed cells that did not express more than 300 genes or had a mitochondrial content greater than 8%. Furthermore  we filtered genes if they were detected in less than 30 cells. Raw counts per cell were normalised to the median count over all cells and transformed into log space to stabilise variance. We initially reduced dimensionality of the dataset using PCA  retaining 50 principal components. Subsequent steps  like low dimensional UMAP embedding and cell clustering  were based on the initial PCA. Final data visualization was done by scanpy and cellxgene packages. Assembly: DanRer11 Supplementary files format and content: starsolo outputs", "heart", null, "Whole hearts were isolated and cardiac cells were dissociated. Dead cells were removed from the final cell isolate by FACs sorting in PBS without xxx and Magnesium and with 0.04% BSA. Each sample was run separately on a lane in a Chromium controller with Chromium Next GEM Single Cell 3\u02b9 Reagent Kits v3 1 10xGenomics.  scRNA seq library preparation was done using a standard protocol  and sequencing was done on a Nextseq2000", null, "tissue:heart|genotype:wild type|age:80hpf", "GSM7764482", "GSM7764482: 80hpf; Danio rerio; RNA Seq", "GSM7764482 r1", "GSM7764482", "1", "Whole hearts were isolated and cardiac cells were dissociated. Dead cells were removed from the final cell isolate by FACs sorting in PBS without xxx and Magnesium and with 0.04% BSA. Each sample was run separately on a lane in a Chromium controller with Chromium Next GEM Single Cell 3\u02b9 Reagent Kits v3 1 10xGenomics.  scRNA seq library preparation was done using a standard protocol  and sequencing was done on a Nextseq2000", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP458853", null, null, "Giulia_80hpf_S2_R1_001.fastq.gz Giulia_80hpf_S2_R2_001.fastq.gz", "fastq fastq", 18811433188.0, 225273324.0, "GSM7764482 r1", "0:28 1:55.50", "A:5135587480;C:4020079745;G:4129712330;T:5427444755;N:98608878", 28, 55, null, null, 5135587480, 4020079745, 4129712330, 5427444755, 98608878, "SRX21649989", "SRS18818461", "SRA1706674", "Bioinformatics, Max-Planck-Institute for Heart and Lung Research", "Bioinformatics, Max-Planck-Institute for Heart and Lung Research", 2, 0.00187, 0.93611, 0.00071, 0.16105, 0.99626, 0.79825, 0.41545, 0.50249, 28, 55, "T", "B", "sc-like readlen", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2023-09-06", "Larval", "Larval", "Heart", "Cardiovascular System"], [28771, "SRR26639098", "SRX22339478", "SRS19389127", "SRP469857", "PRJNA1034995", "Spinster homolog 1 spns1 dependent endocardial autophagy lysosomal pathway drives valve morphogenesis through the control of Notch1 signaling.", "GSE246850", "Transcriptome Analysis", "Autophagy lysosomal degradation is an evolutionarily conserved process key to cellular homeostasis  differentiation  and stress survival  which is particularly important to the pathophysiology of the cardiovascular system. What is more  both experimental and clinical observations indicate that autophagy lysosomal degradation affects correct cardiac morphogenesis  and in particular valve development. However  it is still unclear which cells upregulate autophagy lysosomal degradation and for which specific cellular processes it is required.  Here  we introduce novel zebrafish transgenic models to visualize autophagosomes and lysosomes in vivo and to follow their temporal and cellular localization in the larval heart. This allowed us to determine the kinetics of autophagosome and lysosome vesicle formation and to observe  significant accumulation of lysosomal vesicles during the development of the atrioventricular and bulboventricular valves. We then addressed the functional role of lysosomal degradation in cardiovascular development using a spns1 mutant as a zebrafish model of lysosomal impairment. We found that spns1 mutants displayed morphologically and functionally abnormal heart development  including abnormal endocardial organization  impaired cardiac valve formation and high incidence of retrograde blood flow. Single nuclear transcriptome analysis revealed endocardial specific differences in the expression of lysosome related genes and alterations of notch1 signaling in the mutant larval heart. Further  endocardial specific overexpression of spns1 and notch1 rescued features of valve formation and function as well as overall cardiac morphogenesis. Altogether  our study provides an improved description of the autophagy and lysosomal events that take place during zebrafish heart development and reveals a cell autonomous role of lysosomal processing during cardiac valve formation upstream of notch1 signaling. Overall design: Sibling and spns mutant zebrafish larval hearts were obtained at 3 dpf by manual dissection. Two replicates  each consisting of four pools50 hearts  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ \u00b5L were prepared using the Chromium Nuclei Isolation Kit. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000.", null, "pubmed:39720516", null, "sibling  replicate 2  snRNAseq", "GSM7880035", null, "source name:heart|tissue:heart|age:3dpf|genotype:wt sibling|geo loc name:missing|collection date:missing", "sibling  replicate 2  snRNAseq", "The quality of the sequencing runs was assessed using Illumina Sequencing Analysis Viewer Illumina version 2.4.7 and all base call files were demultiplexed and converted into FASTQ files using Illumina bcl2fastq conversion software v2.20. The raw sequencing data was processed using cellranger v6.0  or demultiplexing  barcode processing  gene count processing. For alignment  we used Danio rerio Genome assembly GRCz11 v109 from Ensembl. Furthere downstream processing was done using Seurat v4 in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: barcodes  tab seprated values Supplementary files format and content: feature counts  tab seprated values Supplementary files format and content: matrix  matrix", "heart", null, "Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described\u200b65\u200b. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific  supplemented with 10% fetal bovine serum Sigma  Aldrich  F7524  centrifuged for 4 minutes at 300 g  snap frozen and preserved in liquid nitrogen. Two replicates  each consisting of four pools  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ \u00b5L were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics  PN 1000494 following the samples Prep User Guide 10 x Genomics  CG000505  Rev A. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics  CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step  GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at  80\u00b0 C. When samples were retrieved from storage  they were cleaned up as stipulated in step 3.0 of the user guide. Therepost  a pre amplification step was performed with 6 PCR cycles  followed by cDNA amplification and 3\u2019 gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific  Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent  DNF 473  respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000. The read set up was as follows: read 1: 29 cycles  i7 index: 10 cycles  i5: 10 cycles and read 2: 89 91 cycles. snRNA seq", null, "tissue:heart|age:3dpf|genotype:wt sibling", "GSM7880035", "GSM7880035: sibling  replicate 2  snRNAseq; Danio rerio; RNA Seq", "GSM7880035 r1", "GSM7880035", "1", "Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described\u200b65\u200b. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific  supplemented with 10% fetal bovine serum Sigma  Aldrich  F7524  centrifuged for 4 minutes at 300 g  snap frozen and preserved in liquid nitrogen. Two replicates  each consisting of four pools  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ \u00b5L were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics  PN 1000494 following the samples Prep User Guide 10 x Genomics  CG000505  Rev A. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics  CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step  GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at  80\u00b0 C. When samples were retrieved from storage  they were cleaned up as stipulated in step 3.0 of the user guide. Therepost  a pre amplification step was performed with 6 PCR cycles  followed by cDNA amplification and three prime gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific  Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent  DNF 473  respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000. The read set up was as follows: read 1: 29 cycles  i7 index: 10 cycles  i5: 10 cycles and read 2: 89 91 cycles. snRNA seq", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP469857", null, "loader:fastq load.py", "sib_2_S1_L001_R1_001.fastq.gz sib_2_S1_L001_R2_001.fastq.gz", "fastq fastq", 29585942468.0, 250728326.0, "GSM7880035 r1", "0:29 1:89", "A:8869085825;C:6519678188;G:6681924988;T:7515095066;N:158401", 29, 89, null, null, 8869085825, 6519678188, 6681924988, 7515095066, 158401, "SRX22339478", "SRS19389127", "SRA1744308", "University of Bern", "University of Bern", 2, 0.03708, 0.89742, 0.02638, 0.33817, 0.98766, 0.87265, 0.50529, 0.84547, 29, 89, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Switzerland", "2023-11-02", "Larval", "Larval", "Heart", "Cardiovascular System"], [28772, "SRR26639099", "SRX22339478", "SRS19389127", "SRP469857", "PRJNA1034995", "Spinster homolog 1 spns1 dependent endocardial autophagy lysosomal pathway drives valve morphogenesis through the control of Notch1 signaling.", "GSE246850", "Transcriptome Analysis", "Autophagy lysosomal degradation is an evolutionarily conserved process key to cellular homeostasis  differentiation  and stress survival  which is particularly important to the pathophysiology of the cardiovascular system. What is more  both experimental and clinical observations indicate that autophagy lysosomal degradation affects correct cardiac morphogenesis  and in particular valve development. However  it is still unclear which cells upregulate autophagy lysosomal degradation and for which specific cellular processes it is required.  Here  we introduce novel zebrafish transgenic models to visualize autophagosomes and lysosomes in vivo and to follow their temporal and cellular localization in the larval heart. This allowed us to determine the kinetics of autophagosome and lysosome vesicle formation and to observe  significant accumulation of lysosomal vesicles during the development of the atrioventricular and bulboventricular valves. We then addressed the functional role of lysosomal degradation in cardiovascular development using a spns1 mutant as a zebrafish model of lysosomal impairment. We found that spns1 mutants displayed morphologically and functionally abnormal heart development  including abnormal endocardial organization  impaired cardiac valve formation and high incidence of retrograde blood flow. Single nuclear transcriptome analysis revealed endocardial specific differences in the expression of lysosome related genes and alterations of notch1 signaling in the mutant larval heart. Further  endocardial specific overexpression of spns1 and notch1 rescued features of valve formation and function as well as overall cardiac morphogenesis. Altogether  our study provides an improved description of the autophagy and lysosomal events that take place during zebrafish heart development and reveals a cell autonomous role of lysosomal processing during cardiac valve formation upstream of notch1 signaling. Overall design: Sibling and spns mutant zebrafish larval hearts were obtained at 3 dpf by manual dissection. Two replicates  each consisting of four pools50 hearts  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ \u00b5L were prepared using the Chromium Nuclei Isolation Kit. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000.", null, "pubmed:39720516", null, "sibling  replicate 2  snRNAseq", "GSM7880035", null, "source name:heart|tissue:heart|age:3dpf|genotype:wt sibling|geo loc name:missing|collection date:missing", "sibling  replicate 2  snRNAseq", "The quality of the sequencing runs was assessed using Illumina Sequencing Analysis Viewer Illumina version 2.4.7 and all base call files were demultiplexed and converted into FASTQ files using Illumina bcl2fastq conversion software v2.20. The raw sequencing data was processed using cellranger v6.0  or demultiplexing  barcode processing  gene count processing. For alignment  we used Danio rerio Genome assembly GRCz11 v109 from Ensembl. Furthere downstream processing was done using Seurat v4 in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: barcodes  tab seprated values Supplementary files format and content: feature counts  tab seprated values Supplementary files format and content: matrix  matrix", "heart", null, "Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described\u200b65\u200b. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific  supplemented with 10% fetal bovine serum Sigma  Aldrich  F7524  centrifuged for 4 minutes at 300 g  snap frozen and preserved in liquid nitrogen. Two replicates  each consisting of four pools  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ \u00b5L were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics  PN 1000494 following the samples Prep User Guide 10 x Genomics  CG000505  Rev A. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics  CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step  GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at  80\u00b0 C. When samples were retrieved from storage  they were cleaned up as stipulated in step 3.0 of the user guide. Therepost  a pre amplification step was performed with 6 PCR cycles  followed by cDNA amplification and 3\u2019 gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific  Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent  DNF 473  respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000. The read set up was as follows: read 1: 29 cycles  i7 index: 10 cycles  i5: 10 cycles and read 2: 89 91 cycles. snRNA seq", null, "tissue:heart|age:3dpf|genotype:wt sibling", "GSM7880035", "GSM7880035: sibling  replicate 2  snRNAseq; Danio rerio; RNA Seq", "GSM7880035 r1", "GSM7880035", "1", "Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described\u200b65\u200b. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific  supplemented with 10% fetal bovine serum Sigma  Aldrich  F7524  centrifuged for 4 minutes at 300 g  snap frozen and preserved in liquid nitrogen. Two replicates  each consisting of four pools  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ \u00b5L were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics  PN 1000494 following the samples Prep User Guide 10 x Genomics  CG000505  Rev A. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics  CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step  GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at  80\u00b0 C. When samples were retrieved from storage  they were cleaned up as stipulated in step 3.0 of the user guide. Therepost  a pre amplification step was performed with 6 PCR cycles  followed by cDNA amplification and three prime gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific  Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent  DNF 473  respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000. The read set up was as follows: read 1: 29 cycles  i7 index: 10 cycles  i5: 10 cycles and read 2: 89 91 cycles. snRNA seq", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP469857", null, "loader:fastq load.py", "sib_2_S1_L002_R1_001.fastq.gz sib_2_S1_L002_R2_001.fastq.gz", "fastq fastq", 29238445684.0, 247783438.0, "GSM7880035 r2", "0:29 1:89", "A:8764474921;C:6441070570;G:6601843083;T:7430828352;N:228758", 29, 89, null, null, 8764474921, 6441070570, 6601843083, 7430828352, 228758, "SRX22339478", "SRS19389127", "SRA1744308", "University of Bern", "University of Bern", 2, 0.03758, 0.89628, 0.02664, 0.33912, 0.98711, 0.87442, 0.4887, 0.42456, 29, 89, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Switzerland", "2023-11-02", "Larval", "Larval", "Heart", "Cardiovascular System"], [28773, "SRR26639100", "SRX22339477", "SRS19389126", "SRP469857", "PRJNA1034995", "Spinster homolog 1 spns1 dependent endocardial autophagy lysosomal pathway drives valve morphogenesis through the control of Notch1 signaling.", "GSE246850", "Transcriptome Analysis", "Autophagy lysosomal degradation is an evolutionarily conserved process key to cellular homeostasis  differentiation  and stress survival  which is particularly important to the pathophysiology of the cardiovascular system. What is more  both experimental and clinical observations indicate that autophagy lysosomal degradation affects correct cardiac morphogenesis  and in particular valve development. However  it is still unclear which cells upregulate autophagy lysosomal degradation and for which specific cellular processes it is required.  Here  we introduce novel zebrafish transgenic models to visualize autophagosomes and lysosomes in vivo and to follow their temporal and cellular localization in the larval heart. This allowed us to determine the kinetics of autophagosome and lysosome vesicle formation and to observe  significant accumulation of lysosomal vesicles during the development of the atrioventricular and bulboventricular valves. We then addressed the functional role of lysosomal degradation in cardiovascular development using a spns1 mutant as a zebrafish model of lysosomal impairment. We found that spns1 mutants displayed morphologically and functionally abnormal heart development  including abnormal endocardial organization  impaired cardiac valve formation and high incidence of retrograde blood flow. Single nuclear transcriptome analysis revealed endocardial specific differences in the expression of lysosome related genes and alterations of notch1 signaling in the mutant larval heart. Further  endocardial specific overexpression of spns1 and notch1 rescued features of valve formation and function as well as overall cardiac morphogenesis. Altogether  our study provides an improved description of the autophagy and lysosomal events that take place during zebrafish heart development and reveals a cell autonomous role of lysosomal processing during cardiac valve formation upstream of notch1 signaling. Overall design: Sibling and spns mutant zebrafish larval hearts were obtained at 3 dpf by manual dissection. Two replicates  each consisting of four pools50 hearts  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ \u00b5L were prepared using the Chromium Nuclei Isolation Kit. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000.", null, "pubmed:39720516", null, "sibling  replicate 1  snRNAseq", "GSM7880034", null, "source name:heart|tissue:heart|age:3dpf|genotype:wt sibling|geo loc name:missing|collection date:missing", "sibling  replicate 1  snRNAseq", "The quality of the sequencing runs was assessed using Illumina Sequencing Analysis Viewer Illumina version 2.4.7 and all base call files were demultiplexed and converted into FASTQ files using Illumina bcl2fastq conversion software v2.20. The raw sequencing data was processed using cellranger v6.0  or demultiplexing  barcode processing  gene count processing. For alignment  we used Danio rerio Genome assembly GRCz11 v109 from Ensembl. Furthere downstream processing was done using Seurat v4 in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: barcodes  tab seprated values Supplementary files format and content: feature counts  tab seprated values Supplementary files format and content: matrix  matrix", "heart", null, "Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described\u200b65\u200b. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific  supplemented with 10% fetal bovine serum Sigma  Aldrich  F7524  centrifuged for 4 minutes at 300 g  snap frozen and preserved in liquid nitrogen. Two replicates  each consisting of four pools  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ \u00b5L were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics  PN 1000494 following the samples Prep User Guide 10 x Genomics  CG000505  Rev A. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics  CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step  GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at  80\u00b0 C. When samples were retrieved from storage  they were cleaned up as stipulated in step 3.0 of the user guide. Therepost  a pre amplification step was performed with 6 PCR cycles  followed by cDNA amplification and 3\u2019 gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific  Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent  DNF 473  respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000. The read set up was as follows: read 1: 29 cycles  i7 index: 10 cycles  i5: 10 cycles and read 2: 89 91 cycles. snRNA seq", null, "tissue:heart|age:3dpf|genotype:wt sibling", "GSM7880034", "GSM7880034: sibling  replicate 1  snRNAseq; Danio rerio; RNA Seq", "GSM7880034 r1", "GSM7880034", "1", "Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described\u200b65\u200b. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific  supplemented with 10% fetal bovine serum Sigma  Aldrich  F7524  centrifuged for 4 minutes at 300 g  snap frozen and preserved in liquid nitrogen. Two replicates  each consisting of four pools  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ \u00b5L were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics  PN 1000494 following the samples Prep User Guide 10 x Genomics  CG000505  Rev A. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics  CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step  GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at  80\u00b0 C. When samples were retrieved from storage  they were cleaned up as stipulated in step 3.0 of the user guide. Therepost  a pre amplification step was performed with 6 PCR cycles  followed by cDNA amplification and three prime gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific  Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent  DNF 473  respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000. The read set up was as follows: read 1: 29 cycles  i7 index: 10 cycles  i5: 10 cycles and read 2: 89 91 cycles. snRNA seq", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP469857", null, "loader:fastq load.py", "sib_1_S1_L001_R1_001.fastq.gz sib_1_S1_L001_R2_001.fastq.gz", "fastq fastq", 24652163520.0, 208916640.0, "GSM7880034 r1", "0:29 1:89", "A:7206225437;C:5487875216;G:5870141423;T:6087790451;N:130993", 29, 89, null, null, 7206225437, 5487875216, 5870141423, 6087790451, 130993, "SRX22339477", "SRS19389126", "SRA1744308", "University of Bern", "University of Bern", 2, 0.04136, 0.8662, 0.02868, 0.3899, 0.98597, 0.86906, 0.42284, 0.79265, 29, 89, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Switzerland", "2023-11-02", "Larval", "Larval", "Heart", "Cardiovascular System"], [28774, "SRR26639101", "SRX22339477", "SRS19389126", "SRP469857", "PRJNA1034995", "Spinster homolog 1 spns1 dependent endocardial autophagy lysosomal pathway drives valve morphogenesis through the control of Notch1 signaling.", "GSE246850", "Transcriptome Analysis", "Autophagy lysosomal degradation is an evolutionarily conserved process key to cellular homeostasis  differentiation  and stress survival  which is particularly important to the pathophysiology of the cardiovascular system. What is more  both experimental and clinical observations indicate that autophagy lysosomal degradation affects correct cardiac morphogenesis  and in particular valve development. However  it is still unclear which cells upregulate autophagy lysosomal degradation and for which specific cellular processes it is required.  Here  we introduce novel zebrafish transgenic models to visualize autophagosomes and lysosomes in vivo and to follow their temporal and cellular localization in the larval heart. This allowed us to determine the kinetics of autophagosome and lysosome vesicle formation and to observe  significant accumulation of lysosomal vesicles during the development of the atrioventricular and bulboventricular valves. We then addressed the functional role of lysosomal degradation in cardiovascular development using a spns1 mutant as a zebrafish model of lysosomal impairment. We found that spns1 mutants displayed morphologically and functionally abnormal heart development  including abnormal endocardial organization  impaired cardiac valve formation and high incidence of retrograde blood flow. Single nuclear transcriptome analysis revealed endocardial specific differences in the expression of lysosome related genes and alterations of notch1 signaling in the mutant larval heart. Further  endocardial specific overexpression of spns1 and notch1 rescued features of valve formation and function as well as overall cardiac morphogenesis. Altogether  our study provides an improved description of the autophagy and lysosomal events that take place during zebrafish heart development and reveals a cell autonomous role of lysosomal processing during cardiac valve formation upstream of notch1 signaling. Overall design: Sibling and spns mutant zebrafish larval hearts were obtained at 3 dpf by manual dissection. Two replicates  each consisting of four pools50 hearts  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ \u00b5L were prepared using the Chromium Nuclei Isolation Kit. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000.", null, "pubmed:39720516", null, "sibling  replicate 1  snRNAseq", "GSM7880034", null, "source name:heart|tissue:heart|age:3dpf|genotype:wt sibling|geo loc name:missing|collection date:missing", "sibling  replicate 1  snRNAseq", "The quality of the sequencing runs was assessed using Illumina Sequencing Analysis Viewer Illumina version 2.4.7 and all base call files were demultiplexed and converted into FASTQ files using Illumina bcl2fastq conversion software v2.20. The raw sequencing data was processed using cellranger v6.0  or demultiplexing  barcode processing  gene count processing. For alignment  we used Danio rerio Genome assembly GRCz11 v109 from Ensembl. Furthere downstream processing was done using Seurat v4 in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: barcodes  tab seprated values Supplementary files format and content: feature counts  tab seprated values Supplementary files format and content: matrix  matrix", "heart", null, "Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described\u200b65\u200b. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific  supplemented with 10% fetal bovine serum Sigma  Aldrich  F7524  centrifuged for 4 minutes at 300 g  snap frozen and preserved in liquid nitrogen. Two replicates  each consisting of four pools  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ \u00b5L were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics  PN 1000494 following the samples Prep User Guide 10 x Genomics  CG000505  Rev A. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics  CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step  GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at  80\u00b0 C. When samples were retrieved from storage  they were cleaned up as stipulated in step 3.0 of the user guide. Therepost  a pre amplification step was performed with 6 PCR cycles  followed by cDNA amplification and 3\u2019 gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific  Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent  DNF 473  respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000. The read set up was as follows: read 1: 29 cycles  i7 index: 10 cycles  i5: 10 cycles and read 2: 89 91 cycles. snRNA seq", null, "tissue:heart|age:3dpf|genotype:wt sibling", "GSM7880034", "GSM7880034: sibling  replicate 1  snRNAseq; Danio rerio; RNA Seq", "GSM7880034 r1", "GSM7880034", "1", "Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described\u200b65\u200b. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific  supplemented with 10% fetal bovine serum Sigma  Aldrich  F7524  centrifuged for 4 minutes at 300 g  snap frozen and preserved in liquid nitrogen. Two replicates  each consisting of four pools  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ \u00b5L were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics  PN 1000494 following the samples Prep User Guide 10 x Genomics  CG000505  Rev A. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics  CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step  GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at  80\u00b0 C. When samples were retrieved from storage  they were cleaned up as stipulated in step 3.0 of the user guide. Therepost  a pre amplification step was performed with 6 PCR cycles  followed by cDNA amplification and three prime gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific  Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent  DNF 473  respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000. The read set up was as follows: read 1: 29 cycles  i7 index: 10 cycles  i5: 10 cycles and read 2: 89 91 cycles. snRNA seq", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP469857", null, "loader:fastq load.py", "sib_1_S1_L002_R1_001.fastq.gz sib_1_S1_L002_R2_001.fastq.gz", "fastq fastq", 24333156656.0, 206213192.0, "GSM7880034 r2", "0:29 1:89", "A:7112369699;C:5414867956;G:5792728480;T:6013000607;N:189914", 29, 89, null, null, 7112369699, 5414867956, 5792728480, 6013000607, 189914, "SRX22339477", "SRS19389126", "SRA1744308", "University of Bern", "University of Bern", 2, 0.04141, 0.86578, 0.02866, 0.39157, 0.98614, 0.8704, 0.42701, 0.78792, 29, 89, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Switzerland", "2023-11-02", "Larval", "Larval", "Heart", "Cardiovascular System"], [28775, "SRR26639102", "SRX22339476", "SRS19389125", "SRP469857", "PRJNA1034995", "Spinster homolog 1 spns1 dependent endocardial autophagy lysosomal pathway drives valve morphogenesis through the control of Notch1 signaling.", "GSE246850", "Transcriptome Analysis", "Autophagy lysosomal degradation is an evolutionarily conserved process key to cellular homeostasis  differentiation  and stress survival  which is particularly important to the pathophysiology of the cardiovascular system. What is more  both experimental and clinical observations indicate that autophagy lysosomal degradation affects correct cardiac morphogenesis  and in particular valve development. However  it is still unclear which cells upregulate autophagy lysosomal degradation and for which specific cellular processes it is required.  Here  we introduce novel zebrafish transgenic models to visualize autophagosomes and lysosomes in vivo and to follow their temporal and cellular localization in the larval heart. This allowed us to determine the kinetics of autophagosome and lysosome vesicle formation and to observe  significant accumulation of lysosomal vesicles during the development of the atrioventricular and bulboventricular valves. We then addressed the functional role of lysosomal degradation in cardiovascular development using a spns1 mutant as a zebrafish model of lysosomal impairment. We found that spns1 mutants displayed morphologically and functionally abnormal heart development  including abnormal endocardial organization  impaired cardiac valve formation and high incidence of retrograde blood flow. Single nuclear transcriptome analysis revealed endocardial specific differences in the expression of lysosome related genes and alterations of notch1 signaling in the mutant larval heart. Further  endocardial specific overexpression of spns1 and notch1 rescued features of valve formation and function as well as overall cardiac morphogenesis. Altogether  our study provides an improved description of the autophagy and lysosomal events that take place during zebrafish heart development and reveals a cell autonomous role of lysosomal processing during cardiac valve formation upstream of notch1 signaling. Overall design: Sibling and spns mutant zebrafish larval hearts were obtained at 3 dpf by manual dissection. Two replicates  each consisting of four pools50 hearts  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ \u00b5L were prepared using the Chromium Nuclei Isolation Kit. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000.", null, "pubmed:39720516", null, "spns mutant  replicate 2  snRNAseq", "GSM7880033", null, "source name:heart|tissue:heart|age:3dpf|genotype:spns mutant|geo loc name:missing|collection date:missing", "spns mutant  replicate 2  snRNAseq", "The quality of the sequencing runs was assessed using Illumina Sequencing Analysis Viewer Illumina version 2.4.7 and all base call files were demultiplexed and converted into FASTQ files using Illumina bcl2fastq conversion software v2.20. The raw sequencing data was processed using cellranger v6.0  or demultiplexing  barcode processing  gene count processing. For alignment  we used Danio rerio Genome assembly GRCz11 v109 from Ensembl. Furthere downstream processing was done using Seurat v4 in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: barcodes  tab seprated values Supplementary files format and content: feature counts  tab seprated values Supplementary files format and content: matrix  matrix", "heart", null, "Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described\u200b65\u200b. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific  supplemented with 10% fetal bovine serum Sigma  Aldrich  F7524  centrifuged for 4 minutes at 300 g  snap frozen and preserved in liquid nitrogen. Two replicates  each consisting of four pools  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ \u00b5L were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics  PN 1000494 following the samples Prep User Guide 10 x Genomics  CG000505  Rev A. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics  CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step  GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at  80\u00b0 C. When samples were retrieved from storage  they were cleaned up as stipulated in step 3.0 of the user guide. Therepost  a pre amplification step was performed with 6 PCR cycles  followed by cDNA amplification and 3\u2019 gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific  Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent  DNF 473  respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000. The read set up was as follows: read 1: 29 cycles  i7 index: 10 cycles  i5: 10 cycles and read 2: 89 91 cycles. snRNA seq", null, "tissue:heart|age:3dpf|genotype:spns mutant", "GSM7880033", "GSM7880033: spns mutant  replicate 2  snRNAseq; Danio rerio; RNA Seq", "GSM7880033 r1", "GSM7880033", "1", "Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described\u200b65\u200b. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific  supplemented with 10% fetal bovine serum Sigma  Aldrich  F7524  centrifuged for 4 minutes at 300 g  snap frozen and preserved in liquid nitrogen. Two replicates  each consisting of four pools  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ \u00b5L were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics  PN 1000494 following the samples Prep User Guide 10 x Genomics  CG000505  Rev A. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics  CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step  GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at  80\u00b0 C. When samples were retrieved from storage  they were cleaned up as stipulated in step 3.0 of the user guide. Therepost  a pre amplification step was performed with 6 PCR cycles  followed by cDNA amplification and three prime gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific  Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent  DNF 473  respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000. The read set up was as follows: read 1: 29 cycles  i7 index: 10 cycles  i5: 10 cycles and read 2: 89 91 cycles. snRNA seq", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP469857", null, "loader:fastq load.py", "mut_2_S1_L001_R1_001.fastq.gz mut_2_S1_L001_R2_001.fastq.gz", "fastq fastq", 33067082062.0, 280229509.0, "GSM7880033 r1", "0:29 1:89", "A:9837791085;C:7302189072;G:7479072379;T:8447851569;N:177957", 29, 89, null, null, 9837791085, 7302189072, 7479072379, 8447851569, 177957, "SRX22339476", "SRS19389125", "SRA1744308", "University of Bern", "University of Bern", 2, 0.03975, 0.89392, 0.02827, 0.35098, 0.98693, 0.87572, 0.42665, 0.8308, 29, 89, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Switzerland", "2023-11-02", "Larval", "Larval", "Heart", "Cardiovascular System"], [28776, "SRR26639103", "SRX22339476", "SRS19389125", "SRP469857", "PRJNA1034995", "Spinster homolog 1 spns1 dependent endocardial autophagy lysosomal pathway drives valve morphogenesis through the control of Notch1 signaling.", "GSE246850", "Transcriptome Analysis", "Autophagy lysosomal degradation is an evolutionarily conserved process key to cellular homeostasis  differentiation  and stress survival  which is particularly important to the pathophysiology of the cardiovascular system. What is more  both experimental and clinical observations indicate that autophagy lysosomal degradation affects correct cardiac morphogenesis  and in particular valve development. However  it is still unclear which cells upregulate autophagy lysosomal degradation and for which specific cellular processes it is required.  Here  we introduce novel zebrafish transgenic models to visualize autophagosomes and lysosomes in vivo and to follow their temporal and cellular localization in the larval heart. This allowed us to determine the kinetics of autophagosome and lysosome vesicle formation and to observe  significant accumulation of lysosomal vesicles during the development of the atrioventricular and bulboventricular valves. We then addressed the functional role of lysosomal degradation in cardiovascular development using a spns1 mutant as a zebrafish model of lysosomal impairment. We found that spns1 mutants displayed morphologically and functionally abnormal heart development  including abnormal endocardial organization  impaired cardiac valve formation and high incidence of retrograde blood flow. Single nuclear transcriptome analysis revealed endocardial specific differences in the expression of lysosome related genes and alterations of notch1 signaling in the mutant larval heart. Further  endocardial specific overexpression of spns1 and notch1 rescued features of valve formation and function as well as overall cardiac morphogenesis. Altogether  our study provides an improved description of the autophagy and lysosomal events that take place during zebrafish heart development and reveals a cell autonomous role of lysosomal processing during cardiac valve formation upstream of notch1 signaling. Overall design: Sibling and spns mutant zebrafish larval hearts were obtained at 3 dpf by manual dissection. Two replicates  each consisting of four pools50 hearts  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ \u00b5L were prepared using the Chromium Nuclei Isolation Kit. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000.", null, "pubmed:39720516", null, "spns mutant  replicate 2  snRNAseq", "GSM7880033", null, "source name:heart|tissue:heart|age:3dpf|genotype:spns mutant|geo loc name:missing|collection date:missing", "spns mutant  replicate 2  snRNAseq", "The quality of the sequencing runs was assessed using Illumina Sequencing Analysis Viewer Illumina version 2.4.7 and all base call files were demultiplexed and converted into FASTQ files using Illumina bcl2fastq conversion software v2.20. The raw sequencing data was processed using cellranger v6.0  or demultiplexing  barcode processing  gene count processing. For alignment  we used Danio rerio Genome assembly GRCz11 v109 from Ensembl. Furthere downstream processing was done using Seurat v4 in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: barcodes  tab seprated values Supplementary files format and content: feature counts  tab seprated values Supplementary files format and content: matrix  matrix", "heart", null, "Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described\u200b65\u200b. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific  supplemented with 10% fetal bovine serum Sigma  Aldrich  F7524  centrifuged for 4 minutes at 300 g  snap frozen and preserved in liquid nitrogen. Two replicates  each consisting of four pools  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ \u00b5L were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics  PN 1000494 following the samples Prep User Guide 10 x Genomics  CG000505  Rev A. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics  CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step  GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at  80\u00b0 C. When samples were retrieved from storage  they were cleaned up as stipulated in step 3.0 of the user guide. Therepost  a pre amplification step was performed with 6 PCR cycles  followed by cDNA amplification and 3\u2019 gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific  Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent  DNF 473  respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000. The read set up was as follows: read 1: 29 cycles  i7 index: 10 cycles  i5: 10 cycles and read 2: 89 91 cycles. snRNA seq", null, "tissue:heart|age:3dpf|genotype:spns mutant", "GSM7880033", "GSM7880033: spns mutant  replicate 2  snRNAseq; Danio rerio; RNA Seq", "GSM7880033 r1", "GSM7880033", "1", "Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described\u200b65\u200b. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific  supplemented with 10% fetal bovine serum Sigma  Aldrich  F7524  centrifuged for 4 minutes at 300 g  snap frozen and preserved in liquid nitrogen. Two replicates  each consisting of four pools  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ \u00b5L were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics  PN 1000494 following the samples Prep User Guide 10 x Genomics  CG000505  Rev A. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics  CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step  GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at  80\u00b0 C. When samples were retrieved from storage  they were cleaned up as stipulated in step 3.0 of the user guide. Therepost  a pre amplification step was performed with 6 PCR cycles  followed by cDNA amplification and three prime gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific  Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent  DNF 473  respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000. The read set up was as follows: read 1: 29 cycles  i7 index: 10 cycles  i5: 10 cycles and read 2: 89 91 cycles. snRNA seq", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP469857", null, "loader:fastq load.py", "mut_2_S1_L002_R1_001.fastq.gz mut_2_S1_L002_R2_001.fastq.gz", "fastq fastq", 32794778418.0, 277921851.0, "GSM7880033 r2", "0:29 1:89", "A:9757463504;C:7238976466;G:7415128557;T:8382951671;N:258220", 29, 89, null, null, 9757463504, 7238976466, 7415128557, 8382951671, 258220, "SRX22339476", "SRS19389125", "SRA1744308", "University of Bern", "University of Bern", 2, 0.04055, 0.89543, 0.02892, 0.35129, 0.98654, 0.87655, 0.45394, 0.85056, 29, 89, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Switzerland", "2023-11-02", "Larval", "Larval", "Heart", "Cardiovascular System"], [28777, "SRR26639104", "SRX22339475", "SRS19389124", "SRP469857", "PRJNA1034995", "Spinster homolog 1 spns1 dependent endocardial autophagy lysosomal pathway drives valve morphogenesis through the control of Notch1 signaling.", "GSE246850", "Transcriptome Analysis", "Autophagy lysosomal degradation is an evolutionarily conserved process key to cellular homeostasis  differentiation  and stress survival  which is particularly important to the pathophysiology of the cardiovascular system. What is more  both experimental and clinical observations indicate that autophagy lysosomal degradation affects correct cardiac morphogenesis  and in particular valve development. However  it is still unclear which cells upregulate autophagy lysosomal degradation and for which specific cellular processes it is required.  Here  we introduce novel zebrafish transgenic models to visualize autophagosomes and lysosomes in vivo and to follow their temporal and cellular localization in the larval heart. This allowed us to determine the kinetics of autophagosome and lysosome vesicle formation and to observe  significant accumulation of lysosomal vesicles during the development of the atrioventricular and bulboventricular valves. We then addressed the functional role of lysosomal degradation in cardiovascular development using a spns1 mutant as a zebrafish model of lysosomal impairment. We found that spns1 mutants displayed morphologically and functionally abnormal heart development  including abnormal endocardial organization  impaired cardiac valve formation and high incidence of retrograde blood flow. Single nuclear transcriptome analysis revealed endocardial specific differences in the expression of lysosome related genes and alterations of notch1 signaling in the mutant larval heart. Further  endocardial specific overexpression of spns1 and notch1 rescued features of valve formation and function as well as overall cardiac morphogenesis. Altogether  our study provides an improved description of the autophagy and lysosomal events that take place during zebrafish heart development and reveals a cell autonomous role of lysosomal processing during cardiac valve formation upstream of notch1 signaling. Overall design: Sibling and spns mutant zebrafish larval hearts were obtained at 3 dpf by manual dissection. Two replicates  each consisting of four pools50 hearts  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ \u00b5L were prepared using the Chromium Nuclei Isolation Kit. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000.", null, "pubmed:39720516", null, "spns mutant  replicate 1  snRNAseq", "GSM7880032", null, "source name:heart|tissue:heart|age:3dpf|genotype:spns mutant|geo loc name:missing|collection date:missing", "spns mutant  replicate 1  snRNAseq", "The quality of the sequencing runs was assessed using Illumina Sequencing Analysis Viewer Illumina version 2.4.7 and all base call files were demultiplexed and converted into FASTQ files using Illumina bcl2fastq conversion software v2.20. The raw sequencing data was processed using cellranger v6.0  or demultiplexing  barcode processing  gene count processing. For alignment  we used Danio rerio Genome assembly GRCz11 v109 from Ensembl. Furthere downstream processing was done using Seurat v4 in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: barcodes  tab seprated values Supplementary files format and content: feature counts  tab seprated values Supplementary files format and content: matrix  matrix", "heart", null, "Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described\u200b65\u200b. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific  supplemented with 10% fetal bovine serum Sigma  Aldrich  F7524  centrifuged for 4 minutes at 300 g  snap frozen and preserved in liquid nitrogen. Two replicates  each consisting of four pools  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ \u00b5L were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics  PN 1000494 following the samples Prep User Guide 10 x Genomics  CG000505  Rev A. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics  CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step  GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at  80\u00b0 C. When samples were retrieved from storage  they were cleaned up as stipulated in step 3.0 of the user guide. Therepost  a pre amplification step was performed with 6 PCR cycles  followed by cDNA amplification and 3\u2019 gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific  Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent  DNF 473  respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000. The read set up was as follows: read 1: 29 cycles  i7 index: 10 cycles  i5: 10 cycles and read 2: 89 91 cycles. snRNA seq", null, "tissue:heart|age:3dpf|genotype:spns mutant", "GSM7880032", "GSM7880032: spns mutant  replicate 1  snRNAseq; Danio rerio; RNA Seq", "GSM7880032 r1", "GSM7880032", "1", "Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described\u200b65\u200b. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific  supplemented with 10% fetal bovine serum Sigma  Aldrich  F7524  centrifuged for 4 minutes at 300 g  snap frozen and preserved in liquid nitrogen. Two replicates  each consisting of four pools  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ \u00b5L were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics  PN 1000494 following the samples Prep User Guide 10 x Genomics  CG000505  Rev A. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics  CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step  GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at  80\u00b0 C. When samples were retrieved from storage  they were cleaned up as stipulated in step 3.0 of the user guide. Therepost  a pre amplification step was performed with 6 PCR cycles  followed by cDNA amplification and three prime gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific  Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent  DNF 473  respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000. The read set up was as follows: read 1: 29 cycles  i7 index: 10 cycles  i5: 10 cycles and read 2: 89 91 cycles. snRNA seq", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP469857", null, "loader:fastq load.py", "mut_1_S1_L001_R1_001.fastq.gz mut_1_S1_L001_R2_001.fastq.gz", "fastq fastq", 30027997254.0, 254474553.0, "GSM7880032 r1", "0:29 1:89", "A:9128230353;C:6473885422;G:6895366272;T:7530354635;N:160572", 29, 89, null, null, 9128230353, 6473885422, 6895366272, 7530354635, 160572, "SRX22339475", "SRS19389124", "SRA1744308", "University of Bern", "University of Bern", 2, 0.03908, 0.86231, 0.0274, 0.38263, 0.98701, 0.87113, 0.48114, 0.78783, 29, 89, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Switzerland", "2023-11-02", "Larval", "Larval", "Heart", "Cardiovascular System"], [28778, "SRR26639105", "SRX22339475", "SRS19389124", "SRP469857", "PRJNA1034995", "Spinster homolog 1 spns1 dependent endocardial autophagy lysosomal pathway drives valve morphogenesis through the control of Notch1 signaling.", "GSE246850", "Transcriptome Analysis", "Autophagy lysosomal degradation is an evolutionarily conserved process key to cellular homeostasis  differentiation  and stress survival  which is particularly important to the pathophysiology of the cardiovascular system. What is more  both experimental and clinical observations indicate that autophagy lysosomal degradation affects correct cardiac morphogenesis  and in particular valve development. However  it is still unclear which cells upregulate autophagy lysosomal degradation and for which specific cellular processes it is required.  Here  we introduce novel zebrafish transgenic models to visualize autophagosomes and lysosomes in vivo and to follow their temporal and cellular localization in the larval heart. This allowed us to determine the kinetics of autophagosome and lysosome vesicle formation and to observe  significant accumulation of lysosomal vesicles during the development of the atrioventricular and bulboventricular valves. We then addressed the functional role of lysosomal degradation in cardiovascular development using a spns1 mutant as a zebrafish model of lysosomal impairment. We found that spns1 mutants displayed morphologically and functionally abnormal heart development  including abnormal endocardial organization  impaired cardiac valve formation and high incidence of retrograde blood flow. Single nuclear transcriptome analysis revealed endocardial specific differences in the expression of lysosome related genes and alterations of notch1 signaling in the mutant larval heart. Further  endocardial specific overexpression of spns1 and notch1 rescued features of valve formation and function as well as overall cardiac morphogenesis. Altogether  our study provides an improved description of the autophagy and lysosomal events that take place during zebrafish heart development and reveals a cell autonomous role of lysosomal processing during cardiac valve formation upstream of notch1 signaling. Overall design: Sibling and spns mutant zebrafish larval hearts were obtained at 3 dpf by manual dissection. Two replicates  each consisting of four pools50 hearts  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ \u00b5L were prepared using the Chromium Nuclei Isolation Kit. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000.", null, "pubmed:39720516", null, "spns mutant  replicate 1  snRNAseq", "GSM7880032", null, "source name:heart|tissue:heart|age:3dpf|genotype:spns mutant|geo loc name:missing|collection date:missing", "spns mutant  replicate 1  snRNAseq", "The quality of the sequencing runs was assessed using Illumina Sequencing Analysis Viewer Illumina version 2.4.7 and all base call files were demultiplexed and converted into FASTQ files using Illumina bcl2fastq conversion software v2.20. The raw sequencing data was processed using cellranger v6.0  or demultiplexing  barcode processing  gene count processing. For alignment  we used Danio rerio Genome assembly GRCz11 v109 from Ensembl. Furthere downstream processing was done using Seurat v4 in R Assembly: GRCz11 v109 Ensembl Supplementary files format and content: barcodes  tab seprated values Supplementary files format and content: feature counts  tab seprated values Supplementary files format and content: matrix  matrix", "heart", null, "Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described\u200b65\u200b. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific  supplemented with 10% fetal bovine serum Sigma  Aldrich  F7524  centrifuged for 4 minutes at 300 g  snap frozen and preserved in liquid nitrogen. Two replicates  each consisting of four pools  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ \u00b5L were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics  PN 1000494 following the samples Prep User Guide 10 x Genomics  CG000505  Rev A. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics  CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step  GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at  80\u00b0 C. When samples were retrieved from storage  they were cleaned up as stipulated in step 3.0 of the user guide. Therepost  a pre amplification step was performed with 6 PCR cycles  followed by cDNA amplification and 3\u2019 gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific  Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent  DNF 473  respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000. The read set up was as follows: read 1: 29 cycles  i7 index: 10 cycles  i5: 10 cycles and read 2: 89 91 cycles. snRNA seq", null, "tissue:heart|age:3dpf|genotype:spns mutant", "GSM7880032", "GSM7880032: spns mutant  replicate 1  snRNAseq; Danio rerio; RNA Seq", "GSM7880032 r1", "GSM7880032", "1", "Sibling and mutant larval hearts were obtained at 3 dpf by manual dissection using forceps and a tungsten needle as previously described\u200b65\u200b. Pools of 50 hearts were collected within one hour in ice cold Leibovitz's L 15 Medium Thermo Fisher Scientific  supplemented with 10% fetal bovine serum Sigma  Aldrich  F7524  centrifuged for 4 minutes at 300 g  snap frozen and preserved in liquid nitrogen. Two replicates  each consisting of four pools  were obtained for each experimental group sibling  mutant. Single nuclei suspensions containing 3800 4000 nuclei/ \u00b5L were prepared using the Chromium Nuclei Isolation Kit with RNase Inhibitor 10 x Genomics  PN 1000494 following the samples Prep User Guide 10 x Genomics  CG000505  Rev A. The Transposition  GEM generation & barcoding  reverse transcription  and preparation of the gene expression and ATAC libraries was performed according to the 4Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide 10x Genomics  CG000338 Rev F with all stipulated 10x Genomics reagents. Nuclei suspensions were incubated in a Transposition Mix that includes a Transposase. At the end of the transposition step  GEM generation and barcoding was immediately performed and then a quenching reagent was added to each sample to stop the reaction. The samples were then stored at  80\u00b0 C. When samples were retrieved from storage  they were cleaned up as stipulated in step 3.0 of the user guide. Therepost  a pre amplification step was performed with 6 PCR cycles  followed by cDNA amplification and three prime gene expression library workflow using 16 PCR cycles. Generated cDNA and both types of libraries were evaluated for quantity and quality using a Thermo Fisher Scientific Qubit 4.0 fluorometer with the Qubit dsDNA HS Assay Kit Thermo Fisher Scientific  Q32851 and an Advanced Analytical Fragment Analyzer System using a Fragment Analyzer NGS Fragment Kit Agilent  DNF 473  respectively. The cDNA libraries were pooled and sequenced with a loading concentration of 300 pM  asymmetric paired end and dual indexed  using an Illumina NovaSeq 6000 S1 Reagent Kit v1.5 100 cycles Illumina  20028319 on an Illumina NovaSeq 6000. The read set up was as follows: read 1: 29 cycles  i7 index: 10 cycles  i5: 10 cycles and read 2: 89 91 cycles. snRNA seq", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP469857", null, "loader:fastq load.py", "mut_1_S1_L002_R1_001.fastq.gz mut_1_S1_L002_R2_001.fastq.gz", "fastq fastq", 29506651188.0, 250056366.0, "GSM7880032 r2", "0:29 1:89", "A:8967217701;C:6359649244;G:6775979696;T:7403576105;N:228442", 29, 89, null, null, 8967217701, 6359649244, 6775979696, 7403576105, 228442, "SRX22339475", "SRS19389124", "SRA1744308", "University of Bern", "University of Bern", 2, 0.03885, 0.86188, 0.02749, 0.38666, 0.98644, 0.86975, 0.46306, 0.79451, 29, 89, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "3prime", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Switzerland", "2023-11-02", "Larval", "Larval", "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"], [30708, "SRR28329751", "SRX23938186", "SRS20741667", "SRP494974", "PRJNA1087264", "Mechanistic Studies of the Regulation of Cardiomyocytes Spatial Distributions by Heterogeneous Erbb2 Expression", "GSE261479", "Transcriptome Analysis", "Purpose: To investigate the mechanism of how Notch Erbb2 signaling coordinated the cardiomyocyte interactions to direct ventricular chamber morphogenesis. Methods:  Approximately 1000 hearts dissected from 96 hpf Tgmyl7:mCherry embryos were collected for RNA sequencing. Results: We found that the expression levels of most genes involved in PI3K AKT signaling and actomyosin structure organization increased prominently. Conclusions: Notch prevents excessive trabeculation by intercepting Erbb2 PI3K signaling pathway. Overall design: 96 hpf Tgmyl7:mCherry zebrafish embryos treated with DMSO or DAPT 100 \u00b5M were collected for RNA seq.", null, "pubmed:40053597", null, "DAPT 3", "GSM8144970", null, "source name:hearts|tissue:hearts|strain:Tgmyl7:mCherry|age:96 hpf|treatment:DAPT|geo loc name:missing|collection date:missing", "DAPT 3", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: Expression matrix  between treatment samples and wild type samples.", "hearts", "60 hpf Tgmyl7:mCherry zebrafish embryos were treated with DMSO or DAPT 100 \u03bcM  to 96 hpf.", "1 \u03bcg total RNA was extracted from Tgmyl7:mCherry zebrafish hearts using TRIzol following the manufacturer\u2019s instruction. RNA libraries were prepared for sequencing using standard Illumina protocols", "Transgenic Tgmyl7:mCherry zebrafish embryos were raised in 0.3x Danieau\u2019s Buffer at 28 \u00b0C with a photoperiod of 14/10\u2009h.", "tissue:hearts|strain:Tgmyl7:mCherry|age:96 hpf|treatment:DAPT", "GSM8144970", "GSM8144970: DAPT 3; Danio rerio; RNA Seq", "GSM8144970 r1", "GSM8144970", "1", "1 \u03bcg total RNA was extracted from Tgmyl7:mCherry zebrafish hearts using TRIzol following the manufacturer's instruction. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP494974", null, null, "DAPT_3_1.fq.gz DAPT_3_2.fq.gz", "fastq fastq", 6899234400.0, 34496172.0, "GSM8144970 r1", "0:100 1:100", "A:1864675679;C:1564709308;G:1588106892;T:1881742521;N:0", 100, 100, null, null, 1864675679, 1564709308, 1588106892, 1881742521, 0, "SRX23938186", "SRS20741667", "SRA1823438", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", 2, 0.93368, 0.93504, 0.09899, 0.09916, 0.67174, 0.67095, 0.51572, 0.5101, 100, 100, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-03-13", "Larval", "Larval", "Heart", "Cardiovascular System"], [30709, "SRR28329752", "SRX23938185", "SRS20741666", "SRP494974", "PRJNA1087264", "Mechanistic Studies of the Regulation of Cardiomyocytes Spatial Distributions by Heterogeneous Erbb2 Expression", "GSE261479", "Transcriptome Analysis", "Purpose: To investigate the mechanism of how Notch Erbb2 signaling coordinated the cardiomyocyte interactions to direct ventricular chamber morphogenesis. Methods:  Approximately 1000 hearts dissected from 96 hpf Tgmyl7:mCherry embryos were collected for RNA sequencing. Results: We found that the expression levels of most genes involved in PI3K AKT signaling and actomyosin structure organization increased prominently. Conclusions: Notch prevents excessive trabeculation by intercepting Erbb2 PI3K signaling pathway. Overall design: 96 hpf Tgmyl7:mCherry zebrafish embryos treated with DMSO or DAPT 100 \u00b5M were collected for RNA seq.", null, "pubmed:40053597", null, "DAPT 2", "GSM8144969", null, "source name:hearts|tissue:hearts|strain:Tgmyl7:mCherry|age:96 hpf|treatment:DAPT|geo loc name:missing|collection date:missing", "DAPT 2", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: Expression matrix  between treatment samples and wild type samples.", "hearts", "60 hpf Tgmyl7:mCherry zebrafish embryos were treated with DMSO or DAPT 100 \u03bcM  to 96 hpf.", "1 \u03bcg total RNA was extracted from Tgmyl7:mCherry zebrafish hearts using TRIzol following the manufacturer\u2019s instruction. RNA libraries were prepared for sequencing using standard Illumina protocols", "Transgenic Tgmyl7:mCherry zebrafish embryos were raised in 0.3x Danieau\u2019s Buffer at 28 \u00b0C with a photoperiod of 14/10\u2009h.", "tissue:hearts|strain:Tgmyl7:mCherry|age:96 hpf|treatment:DAPT", "GSM8144969", "GSM8144969: DAPT 2; Danio rerio; RNA Seq", "GSM8144969 r1", "GSM8144969", "1", "1 \u03bcg total RNA was extracted from Tgmyl7:mCherry zebrafish hearts using TRIzol following the manufacturer's instruction. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP494974", null, null, "DAPT_2_1.fq.gz DAPT_2_2.fq.gz", "fastq fastq", 6920695600.0, 34603478.0, "GSM8144969 r1", "0:100 1:100", "A:1880782056;C:1560368169;G:1581248339;T:1898297036;N:0", 100, 100, null, null, 1880782056, 1560368169, 1581248339, 1898297036, 0, "SRX23938185", "SRS20741666", "SRA1823438", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", 2, 0.93355, 0.93357, 0.10276, 0.10282, 0.67363, 0.67361, 0.51703, 0.52041, 100, 100, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-03-13", "Larval", "Larval", "Heart", "Cardiovascular System"], [30710, "SRR28329753", "SRX23938184", "SRS20741665", "SRP494974", "PRJNA1087264", "Mechanistic Studies of the Regulation of Cardiomyocytes Spatial Distributions by Heterogeneous Erbb2 Expression", "GSE261479", "Transcriptome Analysis", "Purpose: To investigate the mechanism of how Notch Erbb2 signaling coordinated the cardiomyocyte interactions to direct ventricular chamber morphogenesis. Methods:  Approximately 1000 hearts dissected from 96 hpf Tgmyl7:mCherry embryos were collected for RNA sequencing. Results: We found that the expression levels of most genes involved in PI3K AKT signaling and actomyosin structure organization increased prominently. Conclusions: Notch prevents excessive trabeculation by intercepting Erbb2 PI3K signaling pathway. Overall design: 96 hpf Tgmyl7:mCherry zebrafish embryos treated with DMSO or DAPT 100 \u00b5M were collected for RNA seq.", null, "pubmed:40053597", null, "DAPT 1", "GSM8144968", null, "source name:hearts|tissue:hearts|strain:Tgmyl7:mCherry|age:96 hpf|treatment:DAPT|geo loc name:missing|collection date:missing", "DAPT 1", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: Expression matrix  between treatment samples and wild type samples.", "hearts", "60 hpf Tgmyl7:mCherry zebrafish embryos were treated with DMSO or DAPT 100 \u03bcM  to 96 hpf.", "1 \u03bcg total RNA was extracted from Tgmyl7:mCherry zebrafish hearts using TRIzol following the manufacturer\u2019s instruction. RNA libraries were prepared for sequencing using standard Illumina protocols", "Transgenic Tgmyl7:mCherry zebrafish embryos were raised in 0.3x Danieau\u2019s Buffer at 28 \u00b0C with a photoperiod of 14/10\u2009h.", "tissue:hearts|strain:Tgmyl7:mCherry|age:96 hpf|treatment:DAPT", "GSM8144968", "GSM8144968: DAPT 1; Danio rerio; RNA Seq", "GSM8144968 r1", "GSM8144968", "1", "1 \u03bcg total RNA was extracted from Tgmyl7:mCherry zebrafish hearts using TRIzol following the manufacturer's instruction. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP494974", null, null, "DAPT_1_1.fq.gz DAPT_1_2.fq.gz", "fastq fastq", 6917244000.0, 34586220.0, "GSM8144968 r1", "0:100 1:100", "A:1871550461;C:1566067610;G:1585361217;T:1894264712;N:0", 100, 100, null, null, 1871550461, 1566067610, 1585361217, 1894264712, 0, "SRX23938184", "SRS20741665", "SRA1823438", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", 2, 0.9357, 0.93705, 0.09751, 0.09758, 0.67387, 0.67363, 0.51842, 0.51997, 100, 100, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-03-13", "Larval", "Larval", "Heart", "Cardiovascular System"], [30711, "SRR28329754", "SRX23938183", "SRS20741664", "SRP494974", "PRJNA1087264", "Mechanistic Studies of the Regulation of Cardiomyocytes Spatial Distributions by Heterogeneous Erbb2 Expression", "GSE261479", "Transcriptome Analysis", "Purpose: To investigate the mechanism of how Notch Erbb2 signaling coordinated the cardiomyocyte interactions to direct ventricular chamber morphogenesis. Methods:  Approximately 1000 hearts dissected from 96 hpf Tgmyl7:mCherry embryos were collected for RNA sequencing. Results: We found that the expression levels of most genes involved in PI3K AKT signaling and actomyosin structure organization increased prominently. Conclusions: Notch prevents excessive trabeculation by intercepting Erbb2 PI3K signaling pathway. Overall design: 96 hpf Tgmyl7:mCherry zebrafish embryos treated with DMSO or DAPT 100 \u00b5M were collected for RNA seq.", null, "pubmed:40053597", null, "DMSO 3", "GSM8144967", null, "source name:hearts|tissue:hearts|strain:Tgmyl7:mCherry|age:96 hpf|treatment:DMSO|geo loc name:missing|collection date:missing", "DMSO 3", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: Expression matrix  between treatment samples and wild type samples.", "hearts", "60 hpf Tgmyl7:mCherry zebrafish embryos were treated with DMSO or DAPT 100 \u03bcM  to 96 hpf.", "1 \u03bcg total RNA was extracted from Tgmyl7:mCherry zebrafish hearts using TRIzol following the manufacturer\u2019s instruction. RNA libraries were prepared for sequencing using standard Illumina protocols", "Transgenic Tgmyl7:mCherry zebrafish embryos were raised in 0.3x Danieau\u2019s Buffer at 28 \u00b0C with a photoperiod of 14/10\u2009h.", "tissue:hearts|strain:Tgmyl7:mCherry|age:96 hpf|treatment:DMSO", "GSM8144967", "GSM8144967: DMSO 3; Danio rerio; RNA Seq", "GSM8144967 r1", "GSM8144967", "1", "1 \u03bcg total RNA was extracted from Tgmyl7:mCherry zebrafish hearts using TRIzol following the manufacturer's instruction. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP494974", null, null, "DMSO_3_2.fq.gz DMSO_3_1.fq.gz", "fastq fastq", 6919708800.0, 34598544.0, "GSM8144967 r1", "0:100 1:100", "A:1894083722;C:1545002324;G:1569342322;T:1911280432;N:0", 100, 100, null, null, 1894083722, 1545002324, 1569342322, 1911280432, 0, "SRX23938183", "SRS20741664", "SRA1823438", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", 2, 0.93873, 0.93836, 0.10256, 0.10261, 0.66068, 0.6616, 0.52724, 0.52601, 100, 100, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-03-13", "Larval", "Larval", "Heart", "Cardiovascular System"], [30712, "SRR28329755", "SRX23938182", "SRS20741663", "SRP494974", "PRJNA1087264", "Mechanistic Studies of the Regulation of Cardiomyocytes Spatial Distributions by Heterogeneous Erbb2 Expression", "GSE261479", "Transcriptome Analysis", "Purpose: To investigate the mechanism of how Notch Erbb2 signaling coordinated the cardiomyocyte interactions to direct ventricular chamber morphogenesis. Methods:  Approximately 1000 hearts dissected from 96 hpf Tgmyl7:mCherry embryos were collected for RNA sequencing. Results: We found that the expression levels of most genes involved in PI3K AKT signaling and actomyosin structure organization increased prominently. Conclusions: Notch prevents excessive trabeculation by intercepting Erbb2 PI3K signaling pathway. Overall design: 96 hpf Tgmyl7:mCherry zebrafish embryos treated with DMSO or DAPT 100 \u00b5M were collected for RNA seq.", null, "pubmed:40053597", null, "DMSO 2", "GSM8144966", null, "source name:hearts|tissue:hearts|strain:Tgmyl7:mCherry|age:96 hpf|treatment:DMSO|geo loc name:missing|collection date:missing", "DMSO 2", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: Expression matrix  between treatment samples and wild type samples.", "hearts", "60 hpf Tgmyl7:mCherry zebrafish embryos were treated with DMSO or DAPT 100 \u03bcM  to 96 hpf.", "1 \u03bcg total RNA was extracted from Tgmyl7:mCherry zebrafish hearts using TRIzol following the manufacturer\u2019s instruction. RNA libraries were prepared for sequencing using standard Illumina protocols", "Transgenic Tgmyl7:mCherry zebrafish embryos were raised in 0.3x Danieau\u2019s Buffer at 28 \u00b0C with a photoperiod of 14/10\u2009h.", "tissue:hearts|strain:Tgmyl7:mCherry|age:96 hpf|treatment:DMSO", "GSM8144966", "GSM8144966: DMSO 2; Danio rerio; RNA Seq", "GSM8144966 r1", "GSM8144966", "1", "1 \u03bcg total RNA was extracted from Tgmyl7:mCherry zebrafish hearts using TRIzol following the manufacturer's instruction. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP494974", null, null, "DMSO_2_1.fq.gz DMSO_2_2.fq.gz", "fastq fastq", 6902487800.0, 34512439.0, "GSM8144966 r1", "0:100 1:100", "A:1892099736;C:1540950565;G:1559704613;T:1909732886;N:0", 100, 100, null, null, 1892099736, 1540950565, 1559704613, 1909732886, 0, "SRX23938182", "SRS20741663", "SRA1823438", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", 2, 0.93535, 0.93511, 0.10112, 0.10162, 0.66541, 0.66592, 0.51543, 0.51644, 100, 100, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-03-13", "Larval", "Larval", "Heart", "Cardiovascular System"], [30713, "SRR28329756", "SRX23938181", "SRS20741662", "SRP494974", "PRJNA1087264", "Mechanistic Studies of the Regulation of Cardiomyocytes Spatial Distributions by Heterogeneous Erbb2 Expression", "GSE261479", "Transcriptome Analysis", "Purpose: To investigate the mechanism of how Notch Erbb2 signaling coordinated the cardiomyocyte interactions to direct ventricular chamber morphogenesis. Methods:  Approximately 1000 hearts dissected from 96 hpf Tgmyl7:mCherry embryos were collected for RNA sequencing. Results: We found that the expression levels of most genes involved in PI3K AKT signaling and actomyosin structure organization increased prominently. Conclusions: Notch prevents excessive trabeculation by intercepting Erbb2 PI3K signaling pathway. Overall design: 96 hpf Tgmyl7:mCherry zebrafish embryos treated with DMSO or DAPT 100 \u00b5M were collected for RNA seq.", null, "pubmed:40053597", null, "DMSO 1", "GSM8144965", null, "source name:hearts|tissue:hearts|strain:Tgmyl7:mCherry|age:96 hpf|treatment:DMSO|geo loc name:missing|collection date:missing", "DMSO 1", "Illumina sequencing reads were aligned to the Danio rerio genome Ensembl Release 92 GRCz11 using STAR v2.7.1a  and the aligned reads were assigned to each gene using featureCounts v1.6.0. For each embryo  gene counts of each slice were merged into a count matrix  and the genes that received more than 0.5 counts per million reads CPM in at least 3 slices were retained. The count matrixes with slice position information were constructed into DGEList objects using edgeR  which were saved in rds format. Assembly: GRCz11 Supplementary files format and content: Expression matrix  between treatment samples and wild type samples.", "hearts", "60 hpf Tgmyl7:mCherry zebrafish embryos were treated with DMSO or DAPT 100 \u03bcM  to 96 hpf.", "1 \u03bcg total RNA was extracted from Tgmyl7:mCherry zebrafish hearts using TRIzol following the manufacturer\u2019s instruction. RNA libraries were prepared for sequencing using standard Illumina protocols", "Transgenic Tgmyl7:mCherry zebrafish embryos were raised in 0.3x Danieau\u2019s Buffer at 28 \u00b0C with a photoperiod of 14/10\u2009h.", "tissue:hearts|strain:Tgmyl7:mCherry|age:96 hpf|treatment:DMSO", "GSM8144965", "GSM8144965: DMSO 1; Danio rerio; RNA Seq", "GSM8144965 r1", "GSM8144965", "1", "1 \u03bcg total RNA was extracted from Tgmyl7:mCherry zebrafish hearts using TRIzol following the manufacturer's instruction. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP494974", null, null, "DMSO_1_1.fq.gz DMSO_1_2.fq.gz", "fastq fastq", 6918299800.0, 34591499.0, "GSM8144965 r1", "0:100 1:100", "A:1887082093;C:1551476280;G:1575428027;T:1904313400;N:0", 100, 100, null, null, 1887082093, 1551476280, 1575428027, 1904313400, 0, "SRX23938181", "SRS20741662", "SRA1823438", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", 2, 0.93809, 0.93843, 0.098, 0.09793, 0.66647, 0.66709, 0.53463, 0.52582, 100, 100, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2024-03-13", "Larval", "Larval", "Heart", "Cardiovascular System"], [30775, "SRR28357669", "SRX23962905", "SRS20762620", "SRP495490", "PRJNA1088483", "Mechanistic Studies of the Regulation of Cardiomyocytes Spatial Distributions by Heterogeneous Erbb2 Expression [scRNA Seq]", "GSE261718", "Other", "Purpose: To explore the endogenous expression pattern of Erbb2. Methods:  Approximately 1000 hearts dissected from 72 hpf Tgmyl7:mCherry embryos were digested in 0.25% trypsin EDTA solution for single cell RNA sequencing. Results: We found that ventricular Erbb2 expression was highly enriched in subcluster 0 and 2  but weakly expressed in subcluster 3  10 and 12. Conclusions: Erbb2 exhibits heterogeneous expression during trabeculation. Overall design: 72 hpf Tgmyl7:mCherry zebrafish hearts were collected for single cell RNA sequencing.", null, "pubmed:40053597", null, "S72hpf trunks", "GSM8149579", null, "source name:zebrafish hearts|tissue:zebrafish hearts|cell line:Tgmyl7:mCherry heart cells|cell type:zebrafish heart cells|geo loc name:missing|collection date:missing", "S72hpf trunks", "Illumina sequencing reads were aligned to the zebrafish mRNA reference genome GRCz11 using the 10x Genomics CellRanger pipeline version 3.0.2 with default parameters. Assembly: GRCz11 Supplementary files format and content: zip compressed  files include filtered gene bc matrices post running CellRanger pipeline", "zebrafish hearts", null, "A total of 1000 hearts dissected from Tgmyl7:mCherry embryos at 72 hpf were digested in 0.25% trypsin EDTA solution at 37 \u00b0C for 30 min. Single cell RNA seq library construction was performed using a droplet based library prep platform Chromium 10x Genomics with a Chromium Single Cell Reagent Kit according to the manufacturer\u2019s instructions. Single cell RNA Seq 10x", "Dechorionated zebrafish embryos were maintained in 0.3x Danieau\u2019s Buffer at 28 \u00b0C with a photoperiod of 14/10\u2009h light/dark.", "tissue:zebrafish hearts|cell line:Tgmyl7:mCherry heart cells|cell type:zebrafish heart cells", "GSM8149579", "GSM8149579: S72hpf trunks; Danio rerio; RNA Seq", "GSM8149579 r1", "GSM8149579", "1", "A total of 1000 hearts dissected from Tgmyl7:mCherry embryos at 72 hpf were digested in 0.25% trypsin EDTA solution at 37 \u00b0C for 30 min. Single cell RNA seq library construction was performed using a droplet based library prep platform Chromium 10x Genomics with a Chromium Single Cell Reagent Kit according to the manufacturer's instructions. Single cell RNA Seq 10x", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP495490", null, null, "zebrafish_heart_72h_R1_fastq.gz zebrafish_heart_72h_R2_fastq.gz", "fastq fastq", 155978889600.0, 519929632.0, "GSM8149579 r1", "0:150 1:150", "A:63302225780;C:28042347630;G:26792086978;T:37838422350;N:3806862", 150, 150, null, null, 63302225780, 28042347630, 26792086978, 37838422350, 3806862, "SRX23962905", "SRS20762620", "SRA1825277", "Institute of genetics, Zhejiang University", "Institute of genetics, Zhejiang University", 2, 0.0, 0.92044, 0.0, 0.11022, 1.0, 0.80996, null, 0.54499, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2024-03-15", "Larval", "Larval", "Heart", "Cardiovascular System"], [32610, "SRR29325926", "SRX24842083", "SRS21553258", "SRP512516", "PRJNA1121299", "Gene expression profile of single endocardial cells in 48 hpf and 72 hpf zebrafish embryos/larvae. In the study \"The heart is a niche for hematopoietic stem and progenitor cells in zebrafish.\"", "GSE269378", "Transcriptome Analysis", "We used single cell RNA expression to uncover the cellular and molecular heterogeneity of isolated endocardial cells in the heart. From this study  we uncovered the presence of an endocardial hematopoietic cluster  along with other significant clusters including valve endocardial and interstitial cells  and non valve cells. Overall design: Endocardial cells were isolated using FACS from physically extracted Tgkdrl:nls mCherry and Tgcd41:GFP hearts according to presence of mCherry positive cells  and further analyzed using scRNAseq.", null, "pubmed:39217144", null, "EC HC 3d", "GSM8314111", null, "source name:Heart|tissue:Heart|cell type:Endocardial cells|genotype:Tgkdrl:nls mCherry; Tgcd41:GFP|developmental stage:72 hpf loc name:missing|collection date:missing", "EC HC 3d", "Sequencing was done on Nextseq2000 and raw reads were aligned against the zebrafish genome DanRer11 and counted by StarSolo Preprocessed counts were further analysed using Scanpy ollowed by secondary analysis in Annotated Data Format. Preprocessed counts were further analyzed using Scanpy. Basic cell quality control was conducted by taking the number of detected genes and mitochondrial content into consideration. We removed 5 cells in total that did not express more than 300 genes or had a mitochondrial content greater than 5%. Furthermore  we filtered 24259 genes if they were detected in less than 30 cells <0.01%. Raw counts per cell were normalized to the median count over all cells and transformed into log space to stabilize variance. We initially reduced dimensionality of the dataset using PCA  retaining 50 principal components. Subsequent steps  like low dimensional UMAP embedding McInnes & Healy  https://arxiv.org/abs/1802.03426 and cell clustering via community detection  were based on the initial PCA. Final data visualization was done by scanpy and cellxgene packages. Assembly: danRer11 Supplementary files format and content: starsolo outputs", "Heart", null, "Embryos were raised in a solution composed of 0.33 Danieau's medium  containing the following concentrations: 17.4 mM NaCl  0.21 mM KCl  0.12 mM MgSO4\u00b7H2O  and 0.18 mM CaNO32  while being maintained at a stable temperature of 28\u00b0C. To isolate EdCs for the single cell RNA sequencing experiment  hearts from 48  and 72 hpf Tgkdrl:nls mCherry; Tgcd41:GFP larvae were manually dissected in DMEM + 10% FBS.   Hearts were then centrifuged for 60 seconds at 3000 rpm  washed with 1 mL Hanks\u2019 Balanced Salt Solution and dissociated into single cells by incubating in 100 \u03bcl Enzyme 1 and 5 \u03bcl Enzyme 2 Pierce Cardiomyocyte Dissociation Kit  Thermo Fisher Scientific  Cat#88281 for 20 minutes at 300 rpm in a 30\u00b0C shaker 79.  The samples were centrifuged for 5 minutes at 3000 rpm  the supernatant was discarded  and fresh medium was added to the dissociated cells and passed through 40 \u03bcM filter polystyrene 5ml tubes.  Negative controls of non fluorescent hearts or single color fluorescent hearts were prepared to define the sorting gates.  Cells were sorted using the BD FACSAria\u2122 III BD Biosciences instrument.   Live cells were selected by exclusion of DAPI using 30mW 405nm excitation paired with 450/50 nm band pass filter.  The software used for sorting and analysis is BD FACSDiva v8.0.1.  Single positive Tgkdrl:nls mCherry+ cells and double positive Tgkdrl:nls mCherry+; Tgcd41:GFP+ cells were sorted and collected into tubes with DMEM + 10% FBS.  Cells from both collected samples were immediately combined and processed for the single cell RNA sequencing.  mCherry fluorescence was measured with 50mW 561nm excitation paired with 610/20nm band pass filter. GFP fluorescence was measured with 50mW 488nm excitation paired with 530/30 band pass filter. The cell suspensions were counted with Moxi cell counter and diluted according to manufacturer\u2019s protocol to obtain 4.000 2d HC and 8.000 3d  10.497 EC  1.569 HC single cell data points per sample  respectively. Each sample was run separately on a lane in Chromium controller with Chromium Next GEM Single Cell 3\u02b9 Reagent Kits v3.1 10xGenomics. Library preparation was conducted according to the manufacturer indications.", "Embryos/larvae were grown in 28 degree incubator until extraction at 48 or 72 hpf", "tissue:Heart|cell type:Endocardial cells|genotype:Tgkdrl:nls mCherry; Tgcd41:GFP|developmental stage:72 hpf", "GSM8314111", "GSM8314111: EC HC 3d; Danio rerio; RNA Seq", "GSM8314111 r1", "GSM8314111", "1", "Embryos were raised in a solution composed of 0.33 Danieau's medium  containing the following concentrations: 17.4 mM NaCl  0.21 mM KCl  0.12 mM MgSO4\u00b7H2O  and 0.18 mM CaNO32  while being maintained at a stable temperature of 28\u00b0C. To isolate EdCs for the single cell RNA sequencing experiment  hearts from 48  and 72 hpf Tgkdrl:nls mCherry; Tgcd41:GFP larvae were manually dissected in DMEM + 10% FBS.   Hearts were then centrifuged for 60 seconds at 3000 rpm  washed with 1 mL Hanks' Balanced Salt Solution and dissociated into single cells by incubating in 100 \u03bcl Enzyme 1 and 5 \u03bcl Enzyme 2 Pierce Cardiomyocyte Dissociation Kit  Thermo Fisher Scientific  Cat#88281 for 20 minutes at 300 rpm in a 30\u00b0C shaker 79.  The samples were centrifuged for 5 minutes at 3000 rpm  the supernatant was discarded  and fresh medium was added to the dissociated cells and passed through 40 \u03bcM filter polystyrene 5ml tubes.  Negative controls of non fluorescent hearts or single color fluorescent hearts were prepared to define the sorting gates.  Cells were sorted using the BD FACSAria\u2122 III BD Biosciences instrument.   Live cells were selected by exclusion of DAPI using 30mW 405nm excitation paired with 450/50 nm band pass filter.  The software used for sorting and analysis is BD FACSDiva v8.0.1.  Single positive Tgkdrl:nls mCherry+ cells and double positive Tgkdrl:nls mCherry+; Tgcd41:GFP+ cells were sorted and collected into tubes with DMEM + 10% FBS.  Cells from both collected samples were immediately combined and processed for the single cell RNA sequencing.  mCherry fluorescence was measured with 50mW 561nm excitation paired with 610/20nm band pass filter. GFP fluorescence was measured with 50mW 488nm excitation paired with 530/30 band pass filter. The cell suspensions were counted with Moxi cell counter and diluted according to manufacturer's protocol to obtain 4.000 2d HC and 8.000 3d  10.497 EC  1.569 HC single cell data points per sample  respectively. Each sample was run separately on a lane in Chromium controller with Chromium Next GEM Single Cell 3\u02b9 Reagent Kits v3.1 10xGenomics. Library preparation was conducted according to the manufacturer indications.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP512516", null, null, "Felix_10x_Lib_EC-HC_3d_R1.fastq.gz Felix_10x_Lib_EC-HC_3d_R2.fastq.gz", "fastq fastq", 34745112542.0, 437132766.0, "GSM8314111 r1", "0:28 1:51.48", "A:9310358713;C:7641472951;G:8108829079;T:9501691105;N:182760694", 28, 51, null, null, 9310358713, 7641472951, 8108829079, 9501691105, 182760694, "SRX24842083", "SRS21553258", "SRA1892449", "MPI for heart and lung research", "MPI for heart and lung research", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2024-06-07", "Larval", "Larval", "Heart", "Cardiovascular System"], [33934, "SRR30947094", "SRX26349630", "SRS22874784", "SRP537826", "PRJNA1171482", "TAK1 operates at the primary cilium in non canonical TGFB/BMP signaling to control heart development", "GSE279246", "Transcriptome Analysis", "Transforming Growth Factor Beta Activated Kinase 1 TAK1/MAP3K7  along with its upstream regulators TAK1 Binding Protein 2 TAB2 and the catalytic alpha subunit of Protein Kinase A PKA Ca/PRKACA  has been identified as a pivotal player in regulation of developmental processes. Haploinsufficiency of TAB2 causes Congenital Heart Disease CHD and rare variants in PKA Ca and TAK1 cause cardioacrofacial dysplasia CAFD  and Frontometaphyseal Dysplasia FMD and cardiospondylocarpofacial syndrome CSCFS  respectively  rare multisystem syndromes  where CHD may appear in the clinical spectrum. We hypothesized that TAK1 plays a significant role in heart development and CHD and addressed this by genetic analysis in CHD patient cohorts and experiments in cell and animal models. Exome sequencing data from 1 471 CHD patients with extracardiac anomalies syndromic CHD  sCHD  2 405 patients with nonsyndromic CHD nsCHD and 45 082 controls showed increased burden of rare TAB2 and TAK1 variants in sCHD  but not in nsCHD. Detailed characterization of tak1 /  and tab2 /  zebrafish mutants revealed cardiac defects dilated atrium  trabeculation defects  tachycardia and reduced contractility as well as  extracardiac developmental anomalies. RNA sequencing of tak1 /  mutant hearts showed downregulation of genes encoding core cardiac transcription factors  sarcomeric proteins and extracellular matrix proteins. Experiments with cell cultures and analysis of zebrafish larvae and gastruloids indicated that TAK1 via TAB2 and PKA Ca is activated at the primary cilium during cardiomyogenesis and that TAK1 activation at this site is enhanced by cardiomyogenic signaling molecules  including ligands of the TGFB/BMP superfamily. Consistent with these findings  CRISPR/Cas9 mediated editing of TAK1 or administration of small molecule inhibitors targeting TAK1 inhibited ciliary signaling and cardiomyocyte differentiation in vitro  while FMD causing mutations in TAK1 reduced its ciliary localization. In conclusion  our data establishes a central role for TAK1 and its upstream regulators in cardiac development and syndromic CHD  coordinated via the primary cilium. Overall design: To investigate the function of tak1 in heart development  we created a zebrafish mutant using CRISPR cas9. Three groups of hearts from 3 dpf tak1 /  and tak1+/+ zebrafish larvae 15 hearts of each genotype respectively were extracted as previously described PMID 25651299 and RNAseq was used to compare the transcription profile between mutant and wild type.", null, null, null, "whole heart  tak1+/+ wild type  replicate #3", "GSM8565205", null, "source name:Whole heart  3 dpf|tissue:Whole heart  3 dpf|genotype:tak1+/+|geo loc name:missing|collection date:missing", "whole heart  tak1+/+ wild type  replicate #3", "post quality filtering  reads were aligned to reference sequence GCF 000002035.6 GRCz11 using HISAT and Bowtie 2. Average mapping ratio with reference genome was 88.50%  average mapping ratio with genes was 74.56%. In total 23966 genes were identified. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: Matrix txt file. Columns: gene id  NCBI; gene symbol; tpm mut 1; tpm mut 2; tpm mut 3; tpm WT 1; tpm WT 2; tpm WT 3. Data is shown as transcripts per million TPM.", "Whole heart  3 dpf", null, "RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI  China. Samples were paired end sequenced using the DNBSEQ platform.", null, "tissue:Whole heart  3 dpf|genotype:tak1+/+", "GSM8565205", "GSM8565205: whole heart  tak1+/+ wild type  replicate #3; Danio rerio; RNA Seq", "GSM8565205 r1", "GSM8565205", "1", "RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI  China. Samples were paired end sequenced using the DNBSEQ platform.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP537826", null, null, "WT_3_1.fq.gz WT_3_2.fq.gz", "fastq fastq", 4449566200.0, 22247831.0, "GSM8565205 r1", "0:100 1:100", "A:1179341017;C:1046638560;G:1046356098;T:1177230525;N:0", 100, 100, null, null, 1179341017, 1046638560, 1046356098, 1177230525, 0, "SRX26349630", "SRS22874784", "SRA1990217", "Department of Cellular and Molecular Medicine, University of Copenhagen", "Department of Cellular and Molecular Medicine, University of Copenhagen", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "Denmark", "2024-10-10", "Larval", "Larval", "Heart", "Cardiovascular System"], [33935, "SRR30947095", "SRX26349629", "SRS22874783", "SRP537826", "PRJNA1171482", "TAK1 operates at the primary cilium in non canonical TGFB/BMP signaling to control heart development", "GSE279246", "Transcriptome Analysis", "Transforming Growth Factor Beta Activated Kinase 1 TAK1/MAP3K7  along with its upstream regulators TAK1 Binding Protein 2 TAB2 and the catalytic alpha subunit of Protein Kinase A PKA Ca/PRKACA  has been identified as a pivotal player in regulation of developmental processes. Haploinsufficiency of TAB2 causes Congenital Heart Disease CHD and rare variants in PKA Ca and TAK1 cause cardioacrofacial dysplasia CAFD  and Frontometaphyseal Dysplasia FMD and cardiospondylocarpofacial syndrome CSCFS  respectively  rare multisystem syndromes  where CHD may appear in the clinical spectrum. We hypothesized that TAK1 plays a significant role in heart development and CHD and addressed this by genetic analysis in CHD patient cohorts and experiments in cell and animal models. Exome sequencing data from 1 471 CHD patients with extracardiac anomalies syndromic CHD  sCHD  2 405 patients with nonsyndromic CHD nsCHD and 45 082 controls showed increased burden of rare TAB2 and TAK1 variants in sCHD  but not in nsCHD. Detailed characterization of tak1 /  and tab2 /  zebrafish mutants revealed cardiac defects dilated atrium  trabeculation defects  tachycardia and reduced contractility as well as  extracardiac developmental anomalies. RNA sequencing of tak1 /  mutant hearts showed downregulation of genes encoding core cardiac transcription factors  sarcomeric proteins and extracellular matrix proteins. Experiments with cell cultures and analysis of zebrafish larvae and gastruloids indicated that TAK1 via TAB2 and PKA Ca is activated at the primary cilium during cardiomyogenesis and that TAK1 activation at this site is enhanced by cardiomyogenic signaling molecules  including ligands of the TGFB/BMP superfamily. Consistent with these findings  CRISPR/Cas9 mediated editing of TAK1 or administration of small molecule inhibitors targeting TAK1 inhibited ciliary signaling and cardiomyocyte differentiation in vitro  while FMD causing mutations in TAK1 reduced its ciliary localization. In conclusion  our data establishes a central role for TAK1 and its upstream regulators in cardiac development and syndromic CHD  coordinated via the primary cilium. Overall design: To investigate the function of tak1 in heart development  we created a zebrafish mutant using CRISPR cas9. Three groups of hearts from 3 dpf tak1 /  and tak1+/+ zebrafish larvae 15 hearts of each genotype respectively were extracted as previously described PMID 25651299 and RNAseq was used to compare the transcription profile between mutant and wild type.", null, null, null, "whole heart  tak1+/+ wild type  replicate #2", "GSM8565204", null, "source name:Whole heart  3 dpf|tissue:Whole heart  3 dpf|genotype:tak1+/+|geo loc name:missing|collection date:missing", "whole heart  tak1+/+ wild type  replicate #2", "post quality filtering  reads were aligned to reference sequence GCF 000002035.6 GRCz11 using HISAT and Bowtie 2. Average mapping ratio with reference genome was 88.50%  average mapping ratio with genes was 74.56%. In total 23966 genes were identified. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: Matrix txt file. Columns: gene id  NCBI; gene symbol; tpm mut 1; tpm mut 2; tpm mut 3; tpm WT 1; tpm WT 2; tpm WT 3. Data is shown as transcripts per million TPM.", "Whole heart  3 dpf", null, "RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI  China. Samples were paired end sequenced using the DNBSEQ platform.", null, "tissue:Whole heart  3 dpf|genotype:tak1+/+", "GSM8565204", "GSM8565204: whole heart  tak1+/+ wild type  replicate #2; Danio rerio; RNA Seq", "GSM8565204 r1", "GSM8565204", "1", "RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI  China. Samples were paired end sequenced using the DNBSEQ platform.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP537826", null, null, "WT_2_1.fq.gz WT_2_2.fq.gz", "fastq fastq", 4519627600.0, 22598138.0, "GSM8565204 r1", "0:100 1:100", "A:1207344552;C:1055139553;G:1056806709;T:1200336786;N:0", 100, 100, null, null, 1207344552, 1055139553, 1056806709, 1200336786, 0, "SRX26349629", "SRS22874783", "SRA1990217", "Department of Cellular and Molecular Medicine, University of Copenhagen", "Department of Cellular and Molecular Medicine, University of Copenhagen", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "Denmark", "2024-10-10", "Larval", "Larval", "Heart", "Cardiovascular System"], [33936, "SRR30947096", "SRX26349628", "SRS22874781", "SRP537826", "PRJNA1171482", "TAK1 operates at the primary cilium in non canonical TGFB/BMP signaling to control heart development", "GSE279246", "Transcriptome Analysis", "Transforming Growth Factor Beta Activated Kinase 1 TAK1/MAP3K7  along with its upstream regulators TAK1 Binding Protein 2 TAB2 and the catalytic alpha subunit of Protein Kinase A PKA Ca/PRKACA  has been identified as a pivotal player in regulation of developmental processes. Haploinsufficiency of TAB2 causes Congenital Heart Disease CHD and rare variants in PKA Ca and TAK1 cause cardioacrofacial dysplasia CAFD  and Frontometaphyseal Dysplasia FMD and cardiospondylocarpofacial syndrome CSCFS  respectively  rare multisystem syndromes  where CHD may appear in the clinical spectrum. We hypothesized that TAK1 plays a significant role in heart development and CHD and addressed this by genetic analysis in CHD patient cohorts and experiments in cell and animal models. Exome sequencing data from 1 471 CHD patients with extracardiac anomalies syndromic CHD  sCHD  2 405 patients with nonsyndromic CHD nsCHD and 45 082 controls showed increased burden of rare TAB2 and TAK1 variants in sCHD  but not in nsCHD. Detailed characterization of tak1 /  and tab2 /  zebrafish mutants revealed cardiac defects dilated atrium  trabeculation defects  tachycardia and reduced contractility as well as  extracardiac developmental anomalies. RNA sequencing of tak1 /  mutant hearts showed downregulation of genes encoding core cardiac transcription factors  sarcomeric proteins and extracellular matrix proteins. Experiments with cell cultures and analysis of zebrafish larvae and gastruloids indicated that TAK1 via TAB2 and PKA Ca is activated at the primary cilium during cardiomyogenesis and that TAK1 activation at this site is enhanced by cardiomyogenic signaling molecules  including ligands of the TGFB/BMP superfamily. Consistent with these findings  CRISPR/Cas9 mediated editing of TAK1 or administration of small molecule inhibitors targeting TAK1 inhibited ciliary signaling and cardiomyocyte differentiation in vitro  while FMD causing mutations in TAK1 reduced its ciliary localization. In conclusion  our data establishes a central role for TAK1 and its upstream regulators in cardiac development and syndromic CHD  coordinated via the primary cilium. Overall design: To investigate the function of tak1 in heart development  we created a zebrafish mutant using CRISPR cas9. Three groups of hearts from 3 dpf tak1 /  and tak1+/+ zebrafish larvae 15 hearts of each genotype respectively were extracted as previously described PMID 25651299 and RNAseq was used to compare the transcription profile between mutant and wild type.", null, null, null, "whole heart  tak1+/+ wild type  replicate #1", "GSM8565203", null, "source name:Whole heart  3 dpf|tissue:Whole heart  3 dpf|genotype:tak1+/+|geo loc name:missing|collection date:missing", "whole heart  tak1+/+ wild type  replicate #1", "post quality filtering  reads were aligned to reference sequence GCF 000002035.6 GRCz11 using HISAT and Bowtie 2. Average mapping ratio with reference genome was 88.50%  average mapping ratio with genes was 74.56%. In total 23966 genes were identified. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: Matrix txt file. Columns: gene id  NCBI; gene symbol; tpm mut 1; tpm mut 2; tpm mut 3; tpm WT 1; tpm WT 2; tpm WT 3. Data is shown as transcripts per million TPM.", "Whole heart  3 dpf", null, "RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI  China. Samples were paired end sequenced using the DNBSEQ platform.", null, "tissue:Whole heart  3 dpf|genotype:tak1+/+", "GSM8565203", "GSM8565203: whole heart  tak1+/+ wild type  replicate #1; Danio rerio; RNA Seq", "GSM8565203 r1", "GSM8565203", "1", "RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI  China. Samples were paired end sequenced using the DNBSEQ platform.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP537826", null, null, "WT_1_1.fq.gz WT_1_2.fq.gz", "fastq fastq", 4496601200.0, 22483006.0, "GSM8565203 r1", "0:100 1:100", "A:1201390946;C:1050348674;G:1051355386;T:1193506194;N:0", 100, 100, null, null, 1201390946, 1050348674, 1051355386, 1193506194, 0, "SRX26349628", "SRS22874781", "SRA1990217", "Department of Cellular and Molecular Medicine, University of Copenhagen", "Department of Cellular and Molecular Medicine, University of Copenhagen", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "Denmark", "2024-10-10", "Larval", "Larval", "Heart", "Cardiovascular System"], [33937, "SRR30947097", "SRX26349627", "SRS22874780", "SRP537826", "PRJNA1171482", "TAK1 operates at the primary cilium in non canonical TGFB/BMP signaling to control heart development", "GSE279246", "Transcriptome Analysis", "Transforming Growth Factor Beta Activated Kinase 1 TAK1/MAP3K7  along with its upstream regulators TAK1 Binding Protein 2 TAB2 and the catalytic alpha subunit of Protein Kinase A PKA Ca/PRKACA  has been identified as a pivotal player in regulation of developmental processes. Haploinsufficiency of TAB2 causes Congenital Heart Disease CHD and rare variants in PKA Ca and TAK1 cause cardioacrofacial dysplasia CAFD  and Frontometaphyseal Dysplasia FMD and cardiospondylocarpofacial syndrome CSCFS  respectively  rare multisystem syndromes  where CHD may appear in the clinical spectrum. We hypothesized that TAK1 plays a significant role in heart development and CHD and addressed this by genetic analysis in CHD patient cohorts and experiments in cell and animal models. Exome sequencing data from 1 471 CHD patients with extracardiac anomalies syndromic CHD  sCHD  2 405 patients with nonsyndromic CHD nsCHD and 45 082 controls showed increased burden of rare TAB2 and TAK1 variants in sCHD  but not in nsCHD. Detailed characterization of tak1 /  and tab2 /  zebrafish mutants revealed cardiac defects dilated atrium  trabeculation defects  tachycardia and reduced contractility as well as  extracardiac developmental anomalies. RNA sequencing of tak1 /  mutant hearts showed downregulation of genes encoding core cardiac transcription factors  sarcomeric proteins and extracellular matrix proteins. Experiments with cell cultures and analysis of zebrafish larvae and gastruloids indicated that TAK1 via TAB2 and PKA Ca is activated at the primary cilium during cardiomyogenesis and that TAK1 activation at this site is enhanced by cardiomyogenic signaling molecules  including ligands of the TGFB/BMP superfamily. Consistent with these findings  CRISPR/Cas9 mediated editing of TAK1 or administration of small molecule inhibitors targeting TAK1 inhibited ciliary signaling and cardiomyocyte differentiation in vitro  while FMD causing mutations in TAK1 reduced its ciliary localization. In conclusion  our data establishes a central role for TAK1 and its upstream regulators in cardiac development and syndromic CHD  coordinated via the primary cilium. Overall design: To investigate the function of tak1 in heart development  we created a zebrafish mutant using CRISPR cas9. Three groups of hearts from 3 dpf tak1 /  and tak1+/+ zebrafish larvae 15 hearts of each genotype respectively were extracted as previously described PMID 25651299 and RNAseq was used to compare the transcription profile between mutant and wild type.", null, null, null, "whole heart  tak1 /  mutant  replicate #3", "GSM8565202", null, "source name:Whole heart  3 dpf|tissue:Whole heart  3 dpf|genotype:tak1 / |geo loc name:missing|collection date:missing", "whole heart  tak1 /  mutant  replicate #3", "post quality filtering  reads were aligned to reference sequence GCF 000002035.6 GRCz11 using HISAT and Bowtie 2. Average mapping ratio with reference genome was 88.50%  average mapping ratio with genes was 74.56%. In total 23966 genes were identified. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: Matrix txt file. Columns: gene id  NCBI; gene symbol; tpm mut 1; tpm mut 2; tpm mut 3; tpm WT 1; tpm WT 2; tpm WT 3. Data is shown as transcripts per million TPM.", "Whole heart  3 dpf", null, "RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI  China. Samples were paired end sequenced using the DNBSEQ platform.", null, "tissue:Whole heart  3 dpf|genotype:tak1 / ", "GSM8565202", "GSM8565202: whole heart  tak1 /  mutant  replicate #3; Danio rerio; RNA Seq", "GSM8565202 r1", "GSM8565202", "1", "RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI  China. Samples were paired end sequenced using the DNBSEQ platform.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP537826", null, null, "mut_3_1.fq.gz mut_3_2.fq.gz", "fastq fastq", 4451759600.0, 22258798.0, "GSM8565202 r1", "0:100 1:100", "A:1167798041;C:1064608876;G:1066460994;T:1152891689;N:0", 100, 100, null, null, 1167798041, 1064608876, 1066460994, 1152891689, 0, "SRX26349627", "SRS22874780", "SRA1990217", "Department of Cellular and Molecular Medicine, University of Copenhagen", "Department of Cellular and Molecular Medicine, University of Copenhagen", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "Denmark", "2024-10-10", "Larval", "Larval", "Heart", "Cardiovascular System"], [33938, "SRR30947098", "SRX26349626", "SRS22874782", "SRP537826", "PRJNA1171482", "TAK1 operates at the primary cilium in non canonical TGFB/BMP signaling to control heart development", "GSE279246", "Transcriptome Analysis", "Transforming Growth Factor Beta Activated Kinase 1 TAK1/MAP3K7  along with its upstream regulators TAK1 Binding Protein 2 TAB2 and the catalytic alpha subunit of Protein Kinase A PKA Ca/PRKACA  has been identified as a pivotal player in regulation of developmental processes. Haploinsufficiency of TAB2 causes Congenital Heart Disease CHD and rare variants in PKA Ca and TAK1 cause cardioacrofacial dysplasia CAFD  and Frontometaphyseal Dysplasia FMD and cardiospondylocarpofacial syndrome CSCFS  respectively  rare multisystem syndromes  where CHD may appear in the clinical spectrum. We hypothesized that TAK1 plays a significant role in heart development and CHD and addressed this by genetic analysis in CHD patient cohorts and experiments in cell and animal models. Exome sequencing data from 1 471 CHD patients with extracardiac anomalies syndromic CHD  sCHD  2 405 patients with nonsyndromic CHD nsCHD and 45 082 controls showed increased burden of rare TAB2 and TAK1 variants in sCHD  but not in nsCHD. Detailed characterization of tak1 /  and tab2 /  zebrafish mutants revealed cardiac defects dilated atrium  trabeculation defects  tachycardia and reduced contractility as well as  extracardiac developmental anomalies. RNA sequencing of tak1 /  mutant hearts showed downregulation of genes encoding core cardiac transcription factors  sarcomeric proteins and extracellular matrix proteins. Experiments with cell cultures and analysis of zebrafish larvae and gastruloids indicated that TAK1 via TAB2 and PKA Ca is activated at the primary cilium during cardiomyogenesis and that TAK1 activation at this site is enhanced by cardiomyogenic signaling molecules  including ligands of the TGFB/BMP superfamily. Consistent with these findings  CRISPR/Cas9 mediated editing of TAK1 or administration of small molecule inhibitors targeting TAK1 inhibited ciliary signaling and cardiomyocyte differentiation in vitro  while FMD causing mutations in TAK1 reduced its ciliary localization. In conclusion  our data establishes a central role for TAK1 and its upstream regulators in cardiac development and syndromic CHD  coordinated via the primary cilium. Overall design: To investigate the function of tak1 in heart development  we created a zebrafish mutant using CRISPR cas9. Three groups of hearts from 3 dpf tak1 /  and tak1+/+ zebrafish larvae 15 hearts of each genotype respectively were extracted as previously described PMID 25651299 and RNAseq was used to compare the transcription profile between mutant and wild type.", null, null, null, "whole heart  tak1 /  mutant  replicate #2", "GSM8565201", null, "source name:Whole heart  3 dpf|tissue:Whole heart  3 dpf|genotype:tak1 / |geo loc name:missing|collection date:missing", "whole heart  tak1 /  mutant  replicate #2", "post quality filtering  reads were aligned to reference sequence GCF 000002035.6 GRCz11 using HISAT and Bowtie 2. Average mapping ratio with reference genome was 88.50%  average mapping ratio with genes was 74.56%. In total 23966 genes were identified. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: Matrix txt file. Columns: gene id  NCBI; gene symbol; tpm mut 1; tpm mut 2; tpm mut 3; tpm WT 1; tpm WT 2; tpm WT 3. Data is shown as transcripts per million TPM.", "Whole heart  3 dpf", null, "RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI  China. Samples were paired end sequenced using the DNBSEQ platform.", null, "tissue:Whole heart  3 dpf|genotype:tak1 / ", "GSM8565201", "GSM8565201: whole heart  tak1 /  mutant  replicate #2; Danio rerio; RNA Seq", "GSM8565201 r1", "GSM8565201", "1", "RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI  China. Samples were paired end sequenced using the DNBSEQ platform.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP537826", null, null, "mut_2_1.fq.gz mut_2_2.fq.gz", "fastq fastq", 4534495200.0, 22672476.0, "GSM8565201 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX26349626", "SRS22874782", "SRA1990217", "Department of Cellular and Molecular Medicine, University of Copenhagen", "Department of Cellular and Molecular Medicine, University of Copenhagen", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "Denmark", "2024-10-10", "Larval", "Larval", "Heart", "Cardiovascular System"], [33939, "SRR30947099", "SRX26349625", "SRS22874779", "SRP537826", "PRJNA1171482", "TAK1 operates at the primary cilium in non canonical TGFB/BMP signaling to control heart development", "GSE279246", "Transcriptome Analysis", "Transforming Growth Factor Beta Activated Kinase 1 TAK1/MAP3K7  along with its upstream regulators TAK1 Binding Protein 2 TAB2 and the catalytic alpha subunit of Protein Kinase A PKA Ca/PRKACA  has been identified as a pivotal player in regulation of developmental processes. Haploinsufficiency of TAB2 causes Congenital Heart Disease CHD and rare variants in PKA Ca and TAK1 cause cardioacrofacial dysplasia CAFD  and Frontometaphyseal Dysplasia FMD and cardiospondylocarpofacial syndrome CSCFS  respectively  rare multisystem syndromes  where CHD may appear in the clinical spectrum. We hypothesized that TAK1 plays a significant role in heart development and CHD and addressed this by genetic analysis in CHD patient cohorts and experiments in cell and animal models. Exome sequencing data from 1 471 CHD patients with extracardiac anomalies syndromic CHD  sCHD  2 405 patients with nonsyndromic CHD nsCHD and 45 082 controls showed increased burden of rare TAB2 and TAK1 variants in sCHD  but not in nsCHD. Detailed characterization of tak1 /  and tab2 /  zebrafish mutants revealed cardiac defects dilated atrium  trabeculation defects  tachycardia and reduced contractility as well as  extracardiac developmental anomalies. RNA sequencing of tak1 /  mutant hearts showed downregulation of genes encoding core cardiac transcription factors  sarcomeric proteins and extracellular matrix proteins. Experiments with cell cultures and analysis of zebrafish larvae and gastruloids indicated that TAK1 via TAB2 and PKA Ca is activated at the primary cilium during cardiomyogenesis and that TAK1 activation at this site is enhanced by cardiomyogenic signaling molecules  including ligands of the TGFB/BMP superfamily. Consistent with these findings  CRISPR/Cas9 mediated editing of TAK1 or administration of small molecule inhibitors targeting TAK1 inhibited ciliary signaling and cardiomyocyte differentiation in vitro  while FMD causing mutations in TAK1 reduced its ciliary localization. In conclusion  our data establishes a central role for TAK1 and its upstream regulators in cardiac development and syndromic CHD  coordinated via the primary cilium. Overall design: To investigate the function of tak1 in heart development  we created a zebrafish mutant using CRISPR cas9. Three groups of hearts from 3 dpf tak1 /  and tak1+/+ zebrafish larvae 15 hearts of each genotype respectively were extracted as previously described PMID 25651299 and RNAseq was used to compare the transcription profile between mutant and wild type.", null, null, null, "whole heart  tak1 /  mutant  replicate #1", "GSM8565200", null, "source name:Whole heart  3 dpf|tissue:Whole heart  3 dpf|genotype:tak1 / |geo loc name:missing|collection date:missing", "whole heart  tak1 /  mutant  replicate #1", "post quality filtering  reads were aligned to reference sequence GCF 000002035.6 GRCz11 using HISAT and Bowtie 2. Average mapping ratio with reference genome was 88.50%  average mapping ratio with genes was 74.56%. In total 23966 genes were identified. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: Matrix txt file. Columns: gene id  NCBI; gene symbol; tpm mut 1; tpm mut 2; tpm mut 3; tpm WT 1; tpm WT 2; tpm WT 3. Data is shown as transcripts per million TPM.", "Whole heart  3 dpf", null, "RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI  China. Samples were paired end sequenced using the DNBSEQ platform.", null, "tissue:Whole heart  3 dpf|genotype:tak1 / ", "GSM8565200", "GSM8565200: whole heart  tak1 /  mutant  replicate #1; Danio rerio; RNA Seq", "GSM8565200 r1", "GSM8565200", "1", "RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI  China. Samples were paired end sequenced using the DNBSEQ platform.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-G400", null, "SRP537826", null, null, "mut_1_1.fq.gz mut_1_2.fq.gz", "fastq fastq", 4425052600.0, 22125263.0, "GSM8565200 r1", "0:100 1:100", "A:1161989932;C:1055452567;G:1055912540;T:1151697561;N:0", 100, 100, null, null, 1161989932, 1055452567, 1055912540, 1151697561, 0, "SRX26349625", "SRS22874779", "SRA1990217", "Department of Cellular and Molecular Medicine, University of Copenhagen", "Department of Cellular and Molecular Medicine, University of Copenhagen", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "Denmark", "2024-10-10", "Larval", "Larval", "Heart", "Cardiovascular System"], [41259, "SRR4017369", "SRX2011203", "SRS1608491", "SRP081209", "PRJNA338400", "Systematic identification and characterization of long non coding RNAs in zebrafish through RNA Seq", "GSE85416", "Transcriptome Analysis", "We sequenced mRNA from embryonic heart of zebrafish larvae 4 dpf  adult heart of 6 mpf WIK fish  and adult muscle of adult fish consisting of both fast twitch and slow twitch fibers. Overall design: Examination of mRNA and long noncoding RNA levels in embryonic heart  adult heart  and adult muscle tissues", null, "pubmed:28455512", null, "embryonic heart 1", "GSM2266456", null, "source name:zebrafish embryonic heart|developmental stage:embryo|tissue:heart|genotype:wild type|age:4 days", "embryonic heart 1", "The flow cells were sequenced as 50\u00d72 paired end reads on an Illumina HiSeq 2000 using TruSeq SBS Sequencing Kit version 3 and HCS version 2.0.12 data collection software. Raw RNA seq reads were aligned to the zebrafish genome assembly Zv9 for each sample using the Ensembl annotation Zv9 Danio rerio.Zv9.79.gtf by TopHat Version 2.0.12 . Each transcriptome was assembled by Cufflinks Version 2.2.1 . FPKM Fragments Per Kilobase of transcript per Million mapped reads was calculated using a protocol from Cufflinks. Isoform exp.diff was the result form Cuffdiff script  and isoforms.fpkm table was the result from Cuffnorm script. Genome build: Zv9", "zebrafish embryonic heart", null, "Tissues were homogenized using a mortar and pestle Fisher Scientific  and total RNA was extracted using TRIzol Sigma according to the manufacturer\u2019s instructions. RNA quality was assessed using a 2100 Bioanalyzer Instrument Agilent Technologies in the Mayo DNA sequencing core facility. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "developmental stage:embryo|tissue:heart|genotype:wild type|age:4 days", "GSM2266456", "GSM2266456: embryonic heart 1; Danio rerio; RNA Seq", "GSM2266456", null, "1", "Tissues were homogenized using a mortar and pestle Fisher Scientific  and total RNA was extracted using TRIzol Sigma according to the manufacturer\u2019s instructions. RNA quality was assessed using a 2100 Bioanalyzer Instrument Agilent Technologies in the Mayo DNA sequencing core facility. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM2266456", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP081209", null, null, "4dpf_embryonic_heart-4.FCD29WDACXX_L8_ITTAGGC.bam.R1.fastq.gz 4dpf_embryonic_heart-4.FCD29WDACXX_L8_ITTAGGC.bam.R2.fastq.gz", "fastq fastq", 4434115848.0, 43471724.0, "GSM2266456 r1", "0:51 1:51", "A:1111247951;C:1116993636;G:1091144647;T:1114643633;N:85981", 51, 51, null, null, 1111247951, 1116993636, 1091144647, 1114643633, 85981, "SRX2011203", "SRS1608491", "SRA451066", "GEO", "University of Maryland", 2, 0.93493, 0.93506, 0.12094, 0.11976, 0.74953, 0.75144, 0.47962, 0.47646, 51, 51, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-08-10", "Larval", "Larval", "Heart", "Cardiovascular System"], [41260, "SRR4017368", "SRX2011202", "SRS1608488", "SRP081209", "PRJNA338400", "Systematic identification and characterization of long non coding RNAs in zebrafish through RNA Seq", "GSE85416", "Transcriptome Analysis", "We sequenced mRNA from embryonic heart of zebrafish larvae 4 dpf  adult heart of 6 mpf WIK fish  and adult muscle of adult fish consisting of both fast twitch and slow twitch fibers. Overall design: Examination of mRNA and long noncoding RNA levels in embryonic heart  adult heart  and adult muscle tissues", null, "pubmed:28455512", null, "embryonic heart 2", "GSM2266455", null, "source name:zebrafish embryonic heart|developmental stage:embryo|tissue:heart|genotype:wild type|age:4 days", "embryonic heart 2", "The flow cells were sequenced as 50\u00d72 paired end reads on an Illumina HiSeq 2000 using TruSeq SBS Sequencing Kit version 3 and HCS version 2.0.12 data collection software. Raw RNA seq reads were aligned to the zebrafish genome assembly Zv9 for each sample using the Ensembl annotation Zv9 Danio rerio.Zv9.79.gtf by TopHat Version 2.0.12 . Each transcriptome was assembled by Cufflinks Version 2.2.1 . FPKM Fragments Per Kilobase of transcript per Million mapped reads was calculated using a protocol from Cufflinks. Isoform exp.diff was the result form Cuffdiff script  and isoforms.fpkm table was the result from Cuffnorm script. Genome build: Zv9", "zebrafish embryonic heart", null, "Tissues were homogenized using a mortar and pestle Fisher Scientific  and total RNA was extracted using TRIzol Sigma according to the manufacturer\u2019s instructions. RNA quality was assessed using a 2100 Bioanalyzer Instrument Agilent Technologies in the Mayo DNA sequencing core facility. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "developmental stage:embryo|tissue:heart|genotype:wild type|age:4 days", "GSM2266455", "GSM2266455: embryonic heart 2; Danio rerio; RNA Seq", "GSM2266455", null, "1", "Tissues were homogenized using a mortar and pestle Fisher Scientific  and total RNA was extracted using TRIzol Sigma according to the manufacturer\u2019s instructions. RNA quality was assessed using a 2100 Bioanalyzer Instrument Agilent Technologies in the Mayo DNA sequencing core facility. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM2266455", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP081209", null, null, "4dpf_embryonic_heart-3.FCD29WDACXX_L7_ICGATGT.bam.R1.fastq.gz 4dpf_embryonic_heart-3.FCD29WDACXX_L7_ICGATGT.bam.R2.fastq.gz", "fastq fastq", 3994817760.0, 39164880.0, "GSM2266455 r1", "0:51 1:51", "A:984074495;C:1022214385;G:1003461979;T:984987096;N:79805", 51, 51, null, null, 984074495, 1022214385, 1003461979, 984987096, 79805, "SRX2011202", "SRS1608488", "SRA451066", "GEO", "University of Maryland", 2, 0.93632, 0.93575, 0.12674, 0.1252, 0.75595, 0.75649, 0.53521, 0.50945, 51, 51, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-08-10", "Larval", "Larval", "Heart", "Cardiovascular System"], [41261, "SRR4017367", "SRX2011201", "SRS1608490", "SRP081209", "PRJNA338400", "Systematic identification and characterization of long non coding RNAs in zebrafish through RNA Seq", "GSE85416", "Transcriptome Analysis", "We sequenced mRNA from embryonic heart of zebrafish larvae 4 dpf  adult heart of 6 mpf WIK fish  and adult muscle of adult fish consisting of both fast twitch and slow twitch fibers. Overall design: Examination of mRNA and long noncoding RNA levels in embryonic heart  adult heart  and adult muscle tissues", null, "pubmed:28455512", null, "embryonic heart 0", "GSM2266454", null, "source name:zebrafish embryonic heart|developmental stage:embryo|tissue:heart|genotype:wild type|age:4 days", "embryonic heart 0", "The flow cells were sequenced as 50\u00d72 paired end reads on an Illumina HiSeq 2000 using TruSeq SBS Sequencing Kit version 3 and HCS version 2.0.12 data collection software. Raw RNA seq reads were aligned to the zebrafish genome assembly Zv9 for each sample using the Ensembl annotation Zv9 Danio rerio.Zv9.79.gtf by TopHat Version 2.0.12 . Each transcriptome was assembled by Cufflinks Version 2.2.1 . FPKM Fragments Per Kilobase of transcript per Million mapped reads was calculated using a protocol from Cufflinks. Isoform exp.diff was the result form Cuffdiff script  and isoforms.fpkm table was the result from Cuffnorm script. Genome build: Zv9", "zebrafish embryonic heart", null, "Tissues were homogenized using a mortar and pestle Fisher Scientific  and total RNA was extracted using TRIzol Sigma according to the manufacturer\u2019s instructions. RNA quality was assessed using a 2100 Bioanalyzer Instrument Agilent Technologies in the Mayo DNA sequencing core facility. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "developmental stage:embryo|tissue:heart|genotype:wild type|age:4 days", "GSM2266454", "GSM2266454: embryonic heart 0; Danio rerio; RNA Seq", "GSM2266454", null, "1", "Tissues were homogenized using a mortar and pestle Fisher Scientific  and total RNA was extracted using TRIzol Sigma according to the manufacturer\u2019s instructions. RNA quality was assessed using a 2100 Bioanalyzer Instrument Agilent Technologies in the Mayo DNA sequencing core facility. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM2266454", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP081209", null, null, "4dpf_embryonic_heart-2.FCD29WDACXX_L6_IATCACG.bam.R1.fastq.gz 4dpf_embryonic_heart-2.FCD29WDACXX_L6_IATCACG.bam.R2.fastq.gz", "fastq fastq", 3803267472.0, 37286936.0, "GSM2266454 r1", "0:51 1:51", "A:931217439;C:976995973;G:962316893;T:932631659;N:105508", 51, 51, null, null, 931217439, 976995973, 962316893, 932631659, 105508, "SRX2011201", "SRS1608490", "SRA451066", "GEO", "University of Maryland", 2, 0.92776, 0.92939, 0.11824, 0.11891, 0.75856, 0.75927, 0.54225, 0.5297, 51, 51, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-08-10", "Larval", "Larval", "Heart", "Cardiovascular System"], [41859, "SRR6384890", "SRX3478480", "SRS2764469", "SRP100425", "PRJNA376117", "Transcriptome Analysis of Zfpm1 Function in Early Zebrafish Embryogenesis and Postembryonic Heart Development", "GSE95118", "Transcriptome Analysis", "Through analyzing RNA seq datasets in zfpm1 mutant embryo 36hpf and maturing heart 21 dpf  we characterized the effects of loss of zfpm1 on the transcriptomic landscape. Overall design: Using RNA seq to identify the downstream genes of zfpm1 on embryogenesis and cardiac chamber maturation.", null, "pubmed:30611731", null, "Zfpm1 21dpf heart rep3", "GSM2892215", null, "source name:heart|strain:TU|tissue:heart|developmental stage:21dpf|genotype:zfpm1 mutant", "Zfpm1 21dpf heart rep3", "Illumina bcl2fastq2 v 2.16.0.10 software was used for base calling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.5. High quality reads were alligned to GRCz10 whole genome using tophat V2.2.1 and bowtie2 v2.2.3 with parameters  q  p 8   no novel juncs  G  o. Raw counts of sequencing reads were generated by using HTSeq v 0.6.1p1. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample", "heart", null, "36hpf zebrafish embryos and 21dpf heart were collected respectively  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs  and then Frag/Prime Buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution  dNTPs and DNA polymerase\u0399. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer\u2019s instructions  then repaired at the tail ends  polyA added and enriched by PCR amplification. Finally  we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.", null, "strain:TU|tissue:heart|developmental stage:21dpf|genotype:zfpm1 mutant", "GSM2892215", "GSM2892215: Zfpm1 21dpf heart rep3; Danio rerio; RNA Seq", "GSM2892215", null, "1", "36hpf zebrafish embryos and 21dpf heart were collected respectively  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs  and then Frag/Prime Buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution  dNTPs and DNA polymerase\u0399. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer's instructions  then repaired at the tail ends  polyA added and enriched by PCR amplification. Finally  we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.", "GEO Accession:GSM2892215", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP100425", null, null, "Zfpm1_heart_RNAseq_rep3_1.fq.gz Zfpm1_heart_RNAseq_rep3_2.fq.gz", "fastq fastq", 7816015200.0, 26053384.0, "GSM2892215 r1", "0:150 1:150", "A:2069370368;C:1834259592;G:1844770941;T:2066284500;N:1329799", 150, 150, null, null, 2069370368, 1834259592, 1844770941, 2066284500, 1329799, "SRX3478480", "SRS2764469", "SRA539171", "GEO", "Xin Lou Lab, Medical School, Nanjing University", 2, 0.94934, 0.95013, 0.07892, 0.07945, 0.71727, 0.72137, 0.50507, 0.50557, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "China", "2017-12-18", "Larval", "Larval", "Heart", "Cardiovascular System"], [41860, "SRR6384889", "SRX3478479", "SRS2764468", "SRP100425", "PRJNA376117", "Transcriptome Analysis of Zfpm1 Function in Early Zebrafish Embryogenesis and Postembryonic Heart Development", "GSE95118", "Transcriptome Analysis", "Through analyzing RNA seq datasets in zfpm1 mutant embryo 36hpf and maturing heart 21 dpf  we characterized the effects of loss of zfpm1 on the transcriptomic landscape. Overall design: Using RNA seq to identify the downstream genes of zfpm1 on embryogenesis and cardiac chamber maturation.", null, "pubmed:30611731", null, "Zfpm1 21dpf heart rep2", "GSM2892214", null, "source name:heart|strain:TU|tissue:heart|developmental stage:21dpf|genotype:zfpm1 mutant", "Zfpm1 21dpf heart rep2", "Illumina bcl2fastq2 v 2.16.0.10 software was used for base calling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.5. High quality reads were alligned to GRCz10 whole genome using tophat V2.2.1 and bowtie2 v2.2.3 with parameters  q  p 8   no novel juncs  G  o. Raw counts of sequencing reads were generated by using HTSeq v 0.6.1p1. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample", "heart", null, "36hpf zebrafish embryos and 21dpf heart were collected respectively  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs  and then Frag/Prime Buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution  dNTPs and DNA polymerase\u0399. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer\u2019s instructions  then repaired at the tail ends  polyA added and enriched by PCR amplification. Finally  we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.", null, "strain:TU|tissue:heart|developmental stage:21dpf|genotype:zfpm1 mutant", "GSM2892214", "GSM2892214: Zfpm1 21dpf heart rep2; Danio rerio; RNA Seq", "GSM2892214", null, "1", "36hpf zebrafish embryos and 21dpf heart were collected respectively  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs  and then Frag/Prime Buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution  dNTPs and DNA polymerase\u0399. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer's instructions  then repaired at the tail ends  polyA added and enriched by PCR amplification. Finally  we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.", "GEO Accession:GSM2892214", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP100425", null, null, "Zfpm1_heart_RNAseq_rep2_2.fq.gz Zfpm1_heart_RNAseq_rep2_1.fq.gz", "fastq fastq", 6730887900.0, 22436293.0, "GSM2892214 r1", "0:150 1:150", "A:1776206645;C:1586469799;G:1595359983;T:1771693512;N:1157961", 150, 150, null, null, 1776206645, 1586469799, 1595359983, 1771693512, 1157961, "SRX3478479", "SRS2764468", "SRA539171", "GEO", "Xin Lou Lab, Medical School, Nanjing University", 2, 0.94995, 0.94881, 0.07751, 0.0776, 0.7108, 0.71526, 0.51984, 0.50583, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "China", "2017-12-18", "Larval", "Larval", "Heart", "Cardiovascular System"], [41861, "SRR6384888", "SRX3478478", "SRS2764467", "SRP100425", "PRJNA376117", "Transcriptome Analysis of Zfpm1 Function in Early Zebrafish Embryogenesis and Postembryonic Heart Development", "GSE95118", "Transcriptome Analysis", "Through analyzing RNA seq datasets in zfpm1 mutant embryo 36hpf and maturing heart 21 dpf  we characterized the effects of loss of zfpm1 on the transcriptomic landscape. Overall design: Using RNA seq to identify the downstream genes of zfpm1 on embryogenesis and cardiac chamber maturation.", null, "pubmed:30611731", null, "Zfpm1 21dpf heart rep1", "GSM2892213", null, "source name:heart|strain:TU|tissue:heart|developmental stage:21dpf|genotype:zfpm1 mutant", "Zfpm1 21dpf heart rep1", "Illumina bcl2fastq2 v 2.16.0.10 software was used for base calling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.5. High quality reads were alligned to GRCz10 whole genome using tophat V2.2.1 and bowtie2 v2.2.3 with parameters  q  p 8   no novel juncs  G  o. Raw counts of sequencing reads were generated by using HTSeq v 0.6.1p1. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample", "heart", null, "36hpf zebrafish embryos and 21dpf heart were collected respectively  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs  and then Frag/Prime Buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution  dNTPs and DNA polymerase\u0399. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer\u2019s instructions  then repaired at the tail ends  polyA added and enriched by PCR amplification. Finally  we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.", null, "strain:TU|tissue:heart|developmental stage:21dpf|genotype:zfpm1 mutant", "GSM2892213", "GSM2892213: Zfpm1 21dpf heart rep1; Danio rerio; RNA Seq", "GSM2892213", null, "1", "36hpf zebrafish embryos and 21dpf heart were collected respectively  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs  and then Frag/Prime Buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution  dNTPs and DNA polymerase\u0399. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer's instructions  then repaired at the tail ends  polyA added and enriched by PCR amplification. Finally  we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.", "GEO Accession:GSM2892213", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP100425", null, null, "Zfpm1_heart_RNAseq_rep1_1.fq.gz Zfpm1_heart_RNAseq_rep1_2.fq.gz", "fastq fastq", 5936614800.0, 19788716.0, "GSM2892213 r1", "0:150 1:150", "A:1616123286;C:1354032331;G:1348383945;T:1617882201;N:193037", 150, 150, null, null, 1616123286, 1354032331, 1348383945, 1617882201, 193037, "SRX3478478", "SRS2764467", "SRA539171", "GEO", "Xin Lou Lab, Medical School, Nanjing University", 2, 0.93121, 0.93134, 0.08641, 0.08612, 0.69501, 0.69751, 0.51182, 0.50932, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "China", "2017-12-18", "Larval", "Larval", "Heart", "Cardiovascular System"], [41862, "SRR6384887", "SRX3478477", "SRS2764466", "SRP100425", "PRJNA376117", "Transcriptome Analysis of Zfpm1 Function in Early Zebrafish Embryogenesis and Postembryonic Heart Development", "GSE95118", "Transcriptome Analysis", "Through analyzing RNA seq datasets in zfpm1 mutant embryo 36hpf and maturing heart 21 dpf  we characterized the effects of loss of zfpm1 on the transcriptomic landscape. Overall design: Using RNA seq to identify the downstream genes of zfpm1 on embryogenesis and cardiac chamber maturation.", null, "pubmed:30611731", null, "Ctrl 21dpf heart rep3", "GSM2892212", null, "source name:heart|strain:TU|tissue:heart|developmental stage:21dpf|genotype:control", "Ctrl 21dpf heart rep3", "Illumina bcl2fastq2 v 2.16.0.10 software was used for base calling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.5. High quality reads were alligned to GRCz10 whole genome using tophat V2.2.1 and bowtie2 v2.2.3 with parameters  q  p 8   no novel juncs  G  o. Raw counts of sequencing reads were generated by using HTSeq v 0.6.1p1. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample", "heart", null, "36hpf zebrafish embryos and 21dpf heart were collected respectively  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs  and then Frag/Prime Buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution  dNTPs and DNA polymerase\u0399. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer\u2019s instructions  then repaired at the tail ends  polyA added and enriched by PCR amplification. Finally  we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.", null, "strain:TU|tissue:heart|developmental stage:21dpf|genotype:control", "GSM2892212", "GSM2892212: Ctrl 21dpf heart rep3; Danio rerio; RNA Seq", "GSM2892212", null, "1", "36hpf zebrafish embryos and 21dpf heart were collected respectively  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs  and then Frag/Prime Buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution  dNTPs and DNA polymerase\u0399. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer's instructions  then repaired at the tail ends  polyA added and enriched by PCR amplification. Finally  we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.", "GEO Accession:GSM2892212", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP100425", null, null, "Ctrl_heart_RNAseq_rep3_1.fq.gz Ctrl_heart_RNAseq_rep3_2.fq.gz", "fastq fastq", 6715383900.0, 22384613.0, "GSM2892212 r1", "0:150 1:150", "A:1758554869;C:1599044471;G:1608050484;T:1748581031;N:1153045", 150, 150, null, null, 1758554869, 1599044471, 1608050484, 1748581031, 1153045, "SRX3478477", "SRS2764466", "SRA539171", "GEO", "Xin Lou Lab, Medical School, Nanjing University", 2, 0.9491, 0.94781, 0.0799, 0.07904, 0.73357, 0.73795, 0.51407, 0.50294, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "China", "2017-12-18", "Larval", "Larval", "Heart", "Cardiovascular System"], [41863, "SRR6384886", "SRX3478476", "SRS2764465", "SRP100425", "PRJNA376117", "Transcriptome Analysis of Zfpm1 Function in Early Zebrafish Embryogenesis and Postembryonic Heart Development", "GSE95118", "Transcriptome Analysis", "Through analyzing RNA seq datasets in zfpm1 mutant embryo 36hpf and maturing heart 21 dpf  we characterized the effects of loss of zfpm1 on the transcriptomic landscape. Overall design: Using RNA seq to identify the downstream genes of zfpm1 on embryogenesis and cardiac chamber maturation.", null, "pubmed:30611731", null, "Ctrl 21dpf heart rep2", "GSM2892211", null, "source name:heart|strain:TU|tissue:heart|developmental stage:21dpf|genotype:control", "Ctrl 21dpf heart rep2", "Illumina bcl2fastq2 v 2.16.0.10 software was used for base calling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.5. High quality reads were alligned to GRCz10 whole genome using tophat V2.2.1 and bowtie2 v2.2.3 with parameters  q  p 8   no novel juncs  G  o. Raw counts of sequencing reads were generated by using HTSeq v 0.6.1p1. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample", "heart", null, "36hpf zebrafish embryos and 21dpf heart were collected respectively  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs  and then Frag/Prime Buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution  dNTPs and DNA polymerase\u0399. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer\u2019s instructions  then repaired at the tail ends  polyA added and enriched by PCR amplification. Finally  we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.", null, "strain:TU|tissue:heart|developmental stage:21dpf|genotype:control", "GSM2892211", "GSM2892211: Ctrl 21dpf heart rep2; Danio rerio; RNA Seq", "GSM2892211", null, "1", "36hpf zebrafish embryos and 21dpf heart were collected respectively  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs  and then Frag/Prime Buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution  dNTPs and DNA polymerase\u0399. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer's instructions  then repaired at the tail ends  polyA added and enriched by PCR amplification. Finally  we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.", "GEO Accession:GSM2892211", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP100425", null, null, "Ctrl_heart_RNAseq_rep2_1.fq.gz Ctrl_heart_RNAseq_rep2_2.fq.gz", "fastq fastq", 7503873000.0, 25012910.0, "GSM2892211 r1", "0:150 1:150", "A:1975436432;C:1780336468;G:1790380856;T:1956431600;N:1287644", 150, 150, null, null, 1975436432, 1780336468, 1790380856, 1956431600, 1287644, "SRX3478476", "SRS2764465", "SRA539171", "GEO", "Xin Lou Lab, Medical School, Nanjing University", 2, 0.95183, 0.95114, 0.05969, 0.05955, 0.74176, 0.74588, 0.49341, 0.49778, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "China", "2017-12-18", "Larval", "Larval", "Heart", "Cardiovascular System"], [41864, "SRR6384885", "SRX3478475", "SRS2764464", "SRP100425", "PRJNA376117", "Transcriptome Analysis of Zfpm1 Function in Early Zebrafish Embryogenesis and Postembryonic Heart Development", "GSE95118", "Transcriptome Analysis", "Through analyzing RNA seq datasets in zfpm1 mutant embryo 36hpf and maturing heart 21 dpf  we characterized the effects of loss of zfpm1 on the transcriptomic landscape. Overall design: Using RNA seq to identify the downstream genes of zfpm1 on embryogenesis and cardiac chamber maturation.", null, "pubmed:30611731", null, "Ctrl 21dpf heart rep1", "GSM2892210", null, "source name:heart|strain:TU|tissue:heart|developmental stage:21dpf|genotype:control", "Ctrl 21dpf heart rep1", "Illumina bcl2fastq2 v 2.16.0.10 software was used for base calling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.5. High quality reads were alligned to GRCz10 whole genome using tophat V2.2.1 and bowtie2 v2.2.3 with parameters  q  p 8   no novel juncs  G  o. Raw counts of sequencing reads were generated by using HTSeq v 0.6.1p1. Genome build: GRCz10 Supplementary files format and content: tab delimited text files include raw counts for each Sample", "heart", null, "36hpf zebrafish embryos and 21dpf heart were collected respectively  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs  and then Frag/Prime Buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution  dNTPs and DNA polymerase\u0399. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer\u2019s instructions  then repaired at the tail ends  polyA added and enriched by PCR amplification. Finally  we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.", null, "strain:TU|tissue:heart|developmental stage:21dpf|genotype:control", "GSM2892210", "GSM2892210: Ctrl 21dpf heart rep1; Danio rerio; RNA Seq", "GSM2892210", null, "1", "36hpf zebrafish embryos and 21dpf heart were collected respectively  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. Magnetic beads with oligodT were used to enrich the mRNAs  and then Frag/Prime Buffer was added to fragment the mRNAs. The short mRNA fragments were used as templates and random hexamers were used to synthesize first strand cDNA. Then double stranded cDNA was synthesized by adding buffer solution  dNTPs and DNA polymerase\u0399. The double stranded cDNAs were purified by DNA clean beads according to the manufacturer's instructions  then repaired at the tail ends  polyA added and enriched by PCR amplification. Finally  we tested the inserts sizes in the cDNA libraries on an Agilent 2100 Bioanalyzer.", "GEO Accession:GSM2892210", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP100425", null, null, "Ctrl_heart_RNAseq_rep1_1.fq.gz Ctrl_heart_RNAseq_rep1_2.fq.gz", "fastq fastq", 6814864500.0, 22716215.0, "GSM2892210 r1", "0:150 1:150", "A:1866471058;C:1546350618;G:1541549692;T:1860269780;N:223352", 150, 150, null, null, 1866471058, 1546350618, 1541549692, 1860269780, 223352, "SRX3478475", "SRS2764464", "SRA539171", "GEO", "Xin Lou Lab, Medical School, Nanjing University", 2, 0.93945, 0.94117, 0.08481, 0.08446, 0.7359, 0.73845, 0.50016, 0.48236, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "trueseq", "bulk", "unknown", "unknown", null, "China", "2017-12-18", "Larval", "Larval", "Heart", "Cardiovascular System"], [43727, "SRR6039673", "SRX3187841", "SRS2515289", "SRP117696", "PRJNA407368", "RNA seq timecourse analysis during zebrafish heart looping morphogenesis", "PRJNA407368", "Other", "During embryogenesis the heart forms as a linear tube that then undergoes multiple simultaneous morphogenetic events to obtain its mature shape. To understand the gene regulatory networks GRNs driving this phase of heart development  during which many congenital heart disease malformations likely arise  we conducted an RNA seq timecourse in zebrafish from 30 hpf to 72 hpf and identified 5861 genes with altered expression. We clustered the genes by temporal expression pattern  identified transcription factor binding motifs enriched in each cluster  and generated a model GRN for the major gene batteries in heart morphogenesis.", null, null, null, null, "C72", null, "time point hpf group:C|multiplex group:4|strain:cmlc2::gfp reporter line|dev stage:72 hpf organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio heart tissue: Time series during heart looping 30   72 hpf", "C72", "C72", "For each replicate  approximately 1600 zebrafish embryos were collected 200 each at 30  36  42  48  54  60  66  72 hpf Hearts were mechanically separated from the embryos and manually pipetted from the media. Isolated hearts were centrifuged briefly and the supernatant removed. 400 ul of Trizol was then added to the pellet and homogenized before storing at  80C. RNA was isolated by phenol chloroform extraction followed by ethanol precipitation. A total of 6 replicate experiments were performed. To ensure sufficient material for library preparation  each of the 3 replicate groups was formed by pooling 2 of the 6 experiments. RNA Seq libraries were constructed from total RNA using the NuGEN Ovation RNA Seq System v2 ultra low input kit.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP117696", null, null, "9499X24_130410_SN141_0670_AD228RACXX_8.txt.gz", "fastq", 1232597200.0, 24651944.0, "9499X24 130410 SN141 0670 AD228RACXX 8.txt.gz", "0:50", "A:314251321;C:291544555;G:296775805;T:329828647;N:196872", 50, null, null, null, 314251321, 291544555, 296775805, 329828647, 196872, "SRX3187841", "SRS2515289", "SRA608458", "University of Utah|Neurobiology and Anatomy", "University of Utah", 1, 0.85915, null, 0.19661, null, 0.77193, null, 0.54788, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-09-14", "Larval", "Larval", "Heart", "Cardiovascular System"], [43738, "SRR6039684", "SRX3187830", "SRS2515278", "SRP117696", "PRJNA407368", "RNA seq timecourse analysis during zebrafish heart looping morphogenesis", "PRJNA407368", "Other", "During embryogenesis the heart forms as a linear tube that then undergoes multiple simultaneous morphogenetic events to obtain its mature shape. To understand the gene regulatory networks GRNs driving this phase of heart development  during which many congenital heart disease malformations likely arise  we conducted an RNA seq timecourse in zebrafish from 30 hpf to 72 hpf and identified 5861 genes with altered expression. We clustered the genes by temporal expression pattern  identified transcription factor binding motifs enriched in each cluster  and generated a model GRN for the major gene batteries in heart morphogenesis.", null, null, null, null, "A72", null, "time point hpf group:A|multiplex group:2|strain:cmlc2::gfp reporter line|dev stage:72 hpf organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio heart tissue: Time series during heart looping 30   72 hpf", "A72", "A72", "For each replicate  approximately 1600 zebrafish embryos were collected 200 each at 30  36  42  48  54  60  66  72 hpf Hearts were mechanically separated from the embryos and manually pipetted from the media. Isolated hearts were centrifuged briefly and the supernatant removed. 400 ul of Trizol was then added to the pellet and homogenized before storing at  80C. RNA was isolated by phenol chloroform extraction followed by ethanol precipitation. A total of 6 replicate experiments were performed. To ensure sufficient material for library preparation  each of the 3 replicate groups was formed by pooling 2 of the 6 experiments. RNA Seq libraries were constructed from total RNA using the NuGEN Ovation RNA Seq System v2 ultra low input kit.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP117696", null, null, "9499X8_130405_SN141_0668_AD2154ACXX_8.txt.gz", "fastq", 1245726350.0, 24914527.0, "9499X8 130405 SN141 0668 AD2154ACXX 8.txt.gz", "0:50", "A:289841562;C:326831788;G:324971093;T:303973349;N:108558", 50, null, null, null, 289841562, 326831788, 324971093, 303973349, 108558, "SRX3187830", "SRS2515278", "SRA608458", "University of Utah|Neurobiology and Anatomy", "University of Utah", 1, 0.33366, null, 0.08879, null, 0.88994, null, 0.71252, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-09-14", "Larval", "Larval", "Heart", "Cardiovascular System"], [43742, "SRR6039688", "SRX3187826", "SRS2515275", "SRP117696", "PRJNA407368", "RNA seq timecourse analysis during zebrafish heart looping morphogenesis", "PRJNA407368", "Other", "During embryogenesis the heart forms as a linear tube that then undergoes multiple simultaneous morphogenetic events to obtain its mature shape. To understand the gene regulatory networks GRNs driving this phase of heart development  during which many congenital heart disease malformations likely arise  we conducted an RNA seq timecourse in zebrafish from 30 hpf to 72 hpf and identified 5861 genes with altered expression. We clustered the genes by temporal expression pattern  identified transcription factor binding motifs enriched in each cluster  and generated a model GRN for the major gene batteries in heart morphogenesis.", null, null, null, null, "B72", null, "time point hpf group:B|multiplex group:3|strain:cmlc2::gfp reporter line|dev stage:72 hpf organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of Danio rerio heart tissue: Time series during heart looping 30   72 hpf", "B72", "B72", "For each replicate  approximately 1600 zebrafish embryos were collected 200 each at 30  36  42  48  54  60  66  72 hpf Hearts were mechanically separated from the embryos and manually pipetted from the media. Isolated hearts were centrifuged briefly and the supernatant removed. 400 ul of Trizol was then added to the pellet and homogenized before storing at  80C. RNA was isolated by phenol chloroform extraction followed by ethanol precipitation. A total of 6 replicate experiments were performed. To ensure sufficient material for library preparation  each of the 3 replicate groups was formed by pooling 2 of the 6 experiments. RNA Seq libraries were constructed from total RNA using the NuGEN Ovation RNA Seq System v2 ultra low input kit.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP117696", null, null, "9499X16_130410_SN141_0670_AD228RACXX_7.txt.gz", "fastq", 1454189100.0, 29083782.0, "9499X16 130410 SN141 0670 AD228RACXX 7.txt.gz", "0:50", "A:351566404;C:363298465;G:371864963;T:367228366;N:230902", 50, null, null, null, 351566404, 363298465, 371864963, 367228366, 230902, "SRX3187826", "SRS2515275", "SRA608458", "University of Utah|Neurobiology and Anatomy", "University of Utah", 1, 0.86742, null, 0.18808, null, 0.80018, null, 0.7503, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-09-14", "Larval", "Larval", "Heart", "Cardiovascular System"], [46217, "SRR6506181", "SRX3594765", "SRS2867192", "SRP131362", "PRJNA431371", "Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and smyd4 mutant zebrafish cardiac transcriptomes", "GSE109553", "Transcriptome Analysis", "Heart tissue mRNA profiles of  50 wild type WT and  50 homozygous smyd4 mutant zebrafish embryos  at 72 hpf created by CRISPR/Cas9 were generated by deep sequencing. Overall design: Heart mRNA profiles of 72 hpf  wild type WT and smdy4 mutant zebrafish were generated by deep sequencing using illumina", null, null, null, "smyd4", "GSM2946171", null, "source name:heart|tissue:heart|strain:Tu|age:72 hpf|genotype:homozygous smyd4 L544Efs*1", "smyd4", "Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step  clean data clean reads were obtained by removing reads containing adapter  reads containing poly N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality. Index  of  the  reference  genome  was  built  using  Bowtie  v2.0.6  and paired end clean reads were aligned to the reference genome using TopHat v2.0.9. RPKM of each gene was calculated based on the length of the gene and reads count mapped to  this  gene  considering the effect of sequencing depth and gene length for the reads count at the same time Mortazavi et al.  2008 Genome build: ftp://ftp.ensembl.org/pub/release 89/fasta/danio rerio/dna/ Supplementary files format and content: text file with RPKM", "heart", null, "zebrafish heart were collected  flash frozen on dry ice  and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:heart|strain:Tu|age:72 hpf|genotype:homozygous smyd4 L544Efs*1", "GSM2946171", "GSM2946171: smyd4; Danio rerio; RNA Seq", "GSM2946171", null, "1", "zebrafish heart were collected  flash frozen on dry ice  and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM2946171", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP131362", null, null, "smyd4_zf_1.fq.gz smyd4_zf_2.fq.gz", "fastq fastq", 7954641600.0, 26515472.0, "GSM2946171 r1", "0:150 1:150", "A:2150119275;C:1788273579;G:1800637070;T:2214193156;N:1418520", 150, 150, null, null, 2150119275, 1788273579, 1800637070, 2214193156, 1418520, "SRX3594765", "SRS2867192", "SRA651951", "GEO", "Fudan university", 2, 0.95241, 0.94978, 0.06519, 0.06325, 0.70838, 0.71587, 0.42753, 0.42209, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2018-01-24", "Larval", "Larval", "Heart", "Cardiovascular System"], [46218, "SRR6506180", "SRX3594764", "SRS2867189", "SRP131362", "PRJNA431371", "Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and smyd4 mutant zebrafish cardiac transcriptomes", "GSE109553", "Transcriptome Analysis", "Heart tissue mRNA profiles of  50 wild type WT and  50 homozygous smyd4 mutant zebrafish embryos  at 72 hpf created by CRISPR/Cas9 were generated by deep sequencing. Overall design: Heart mRNA profiles of 72 hpf  wild type WT and smdy4 mutant zebrafish were generated by deep sequencing using illumina", null, null, null, "wt", "GSM2946170", null, "source name:heart|tissue:heart|strain:Tu|age:72 hpf|genotype:wt", "wt", "Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step  clean data clean reads were obtained by removing reads containing adapter  reads containing poly N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality. Index  of  the  reference  genome  was  built  using  Bowtie  v2.0.6  and paired end clean reads were aligned to the reference genome using TopHat v2.0.9. RPKM of each gene was calculated based on the length of the gene and reads count mapped to  this  gene  considering the effect of sequencing depth and gene length for the reads count at the same time Mortazavi et al.  2008 Genome build: ftp://ftp.ensembl.org/pub/release 89/fasta/danio rerio/dna/ Supplementary files format and content: text file with RPKM", "heart", null, "zebrafish heart were collected  flash frozen on dry ice  and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:heart|strain:Tu|age:72 hpf|genotype:wt", "GSM2946170", "GSM2946170: wt; Danio rerio; RNA Seq", "GSM2946170", null, "1", "zebrafish heart were collected  flash frozen on dry ice  and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM2946170", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP131362", null, null, "ctr_zf_1.fq.gz ctr_zf_2.fq.gz", "fastq fastq", 9601941900.0, 32006473.0, "GSM2946170 r1", "0:150 1:150", "A:2440007788;C:2202792595;G:2248095757;T:2709447485;N:1598275", 150, 150, null, null, 2440007788, 2202792595, 2248095757, 2709447485, 1598275, "SRX3594764", "SRS2867189", "SRA651951", "GEO", "Fudan university", 2, 0.93538, 0.92842, 0.05404, 0.04218, 0.7387, 0.75866, 0.43777, 0.42189, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2018-01-24", "Larval", "Larval", "Heart", "Cardiovascular System"], [48190, "SRR7119875", "SRX4041518", "SRS3258997", "SRP144601", "PRJNA459724", "The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis", "GSE114038", "Other", "Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively", null, "pubmed:30867528", null, "Danio rerio RNAseq singleHeart 3dpf mut 44", "GSM3131266", null, "tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2 / ", "Danio rerio RNAseq singleHeart 3dpf mut 44", "RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "heart", null, "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "Zebrafish Danio rerio  were housed at 27.5\u00b0C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.", "strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2 / ", "GSM3131266", "GSM3131266: Danio rerio RNAseq singleHeart 3dpf mut 44; Danio rerio; RNA Seq", "GSM3131266", null, "1", "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "GEO Accession:GSM3131266", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP144601", null, null, "NDCII_1_44_NDCII_sample_0044.fastq.gz", "fastq", 182748450.0, 2436646.0, "GSM3131266 r1", "0:75", "A:58073626;C:30410206;G:39711272;T:54442336;N:111010", 75, null, null, null, 58073626, 30410206, 39711272, 54442336, 111010, "SRX4041518", "SRS3258997", "SRA699717", "GEO", "Molecular Biology, Radboud University", 1, 0.60972, null, 0.21593, null, 0.85427, null, 0.51332, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-05-04", "Larval", "Larval", "Heart", "Cardiovascular System"], [48191, "SRR7119874", "SRX4041517", "SRS3258996", "SRP144601", "PRJNA459724", "The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis", "GSE114038", "Other", "Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively", null, "pubmed:30867528", null, "Danio rerio RNAseq singleHeart 3dpf mut 43", "GSM3131265", null, "tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2 / ", "Danio rerio RNAseq singleHeart 3dpf mut 43", "RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "heart", null, "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "Zebrafish Danio rerio  were housed at 27.5\u00b0C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.", "strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2 / ", "GSM3131265", "GSM3131265: Danio rerio RNAseq singleHeart 3dpf mut 43; Danio rerio; RNA Seq", "GSM3131265", null, "1", "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "GEO Accession:GSM3131265", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP144601", null, null, "NDCII_1_43_NDCII_sample_0043.fastq.gz", "fastq", 91153575.0, 1215381.0, "GSM3131265 r1", "0:75", "A:29202562;C:14935465;G:19738048;T:27228137;N:49363", 75, null, null, null, 29202562, 14935465, 19738048, 27228137, 49363, "SRX4041517", "SRS3258996", "SRA699717", "GEO", "Molecular Biology, Radboud University", 1, 0.61061, null, 0.18268, null, 0.87257, null, 0.51994, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-05-04", "Larval", "Larval", "Heart", "Cardiovascular System"], [48192, "SRR7119873", "SRX4041516", "SRS3258995", "SRP144601", "PRJNA459724", "The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis", "GSE114038", "Other", "Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively", null, "pubmed:30867528", null, "Danio rerio RNAseq singleHeart 3dpf mut 42", "GSM3131264", null, "tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2 / ", "Danio rerio RNAseq singleHeart 3dpf mut 42", "RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "heart", null, "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "Zebrafish Danio rerio  were housed at 27.5\u00b0C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.", "strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2 / ", "GSM3131264", "GSM3131264: Danio rerio RNAseq singleHeart 3dpf mut 42; Danio rerio; RNA Seq", "GSM3131264", null, "1", "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "GEO Accession:GSM3131264", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP144601", null, null, "NDCII_1_42_NDCII_sample_0042.fastq.gz", "fastq", 213129525.0, 2841727.0, "GSM3131264 r1", "0:75", "A:66201701;C:36179557;G:46211697;T:64412897;N:123673", 75, null, null, null, 66201701, 36179557, 46211697, 64412897, 123673, "SRX4041516", "SRS3258995", "SRA699717", "GEO", "Molecular Biology, Radboud University", 1, 0.62509, null, 0.23068, null, 0.85397, null, 0.4951, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-05-04", "Larval", "Larval", "Heart", "Cardiovascular System"], [48193, "SRR7119872", "SRX4041515", "SRS3258994", "SRP144601", "PRJNA459724", "The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis", "GSE114038", "Other", "Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively", null, "pubmed:30867528", null, "Danio rerio RNAseq singleHeart 3dpf mut 41", "GSM3131263", null, "tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2 / ", "Danio rerio RNAseq singleHeart 3dpf mut 41", "RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "heart", null, "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "Zebrafish Danio rerio  were housed at 27.5\u00b0C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.", "strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2 / ", "GSM3131263", "GSM3131263: Danio rerio RNAseq singleHeart 3dpf mut 41; Danio rerio; RNA Seq", "GSM3131263", null, "1", "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "GEO Accession:GSM3131263", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP144601", null, null, "NDCII_1_41_NDCII_sample_0041.fastq.gz", "fastq", 166984800.0, 2226464.0, "GSM3131263 r1", "0:75", "A:52059221;C:28218639;G:36132669;T:50478431;N:95840", 75, null, null, null, 52059221, 28218639, 36132669, 50478431, 95840, "SRX4041515", "SRS3258994", "SRA699717", "GEO", "Molecular Biology, Radboud University", 1, 0.64245, null, 0.22817, null, 0.86535, null, 0.4946, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-05-04", "Larval", "Larval", "Heart", "Cardiovascular System"], [48194, "SRR7119871", "SRX4041514", "SRS3258992", "SRP144601", "PRJNA459724", "The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis", "GSE114038", "Other", "Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively", null, "pubmed:30867528", null, "Danio rerio RNAseq singleHeart 3dpf mut 40", "GSM3131262", null, "tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2 / ", "Danio rerio RNAseq singleHeart 3dpf mut 40", "RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "heart", null, "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "Zebrafish Danio rerio  were housed at 27.5\u00b0C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.", "strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2 / ", "GSM3131262", "GSM3131262: Danio rerio RNAseq singleHeart 3dpf mut 40; Danio rerio; RNA Seq", "GSM3131262", null, "1", "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "GEO Accession:GSM3131262", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP144601", null, null, "NDCII_1_40_NDCII_sample_0040.fastq.gz", "fastq", 76091325.0, 1014551.0, "GSM3131262 r1", "0:75", "A:23961767;C:13365431;G:16139381;T:22578835;N:45911", 75, null, null, null, 23961767, 13365431, 16139381, 22578835, 45911, "SRX4041514", "SRS3258992", "SRA699717", "GEO", "Molecular Biology, Radboud University", 1, 0.68263, null, 0.15501, null, 0.86642, null, 0.45686, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-05-04", "Larval", "Larval", "Heart", "Cardiovascular System"], [48195, "SRR7119870", "SRX4041513", "SRS3258993", "SRP144601", "PRJNA459724", "The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis", "GSE114038", "Other", "Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively", null, "pubmed:30867528", null, "Danio rerio RNAseq singleHeart 3dpf mut 39", "GSM3131261", null, "tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2 / ", "Danio rerio RNAseq singleHeart 3dpf mut 39", "RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "heart", null, "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "Zebrafish Danio rerio  were housed at 27.5\u00b0C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.", "strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2 / ", "GSM3131261", "GSM3131261: Danio rerio RNAseq singleHeart 3dpf mut 39; Danio rerio; RNA Seq", "GSM3131261", null, "1", "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "GEO Accession:GSM3131261", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP144601", null, null, "NDCII_1_39_NDCII_sample_0039.fastq.gz", "fastq", 83697825.0, 1115971.0, "GSM3131261 r1", "0:75", "A:25833162;C:14319026;G:18237724;T:25260425;N:47488", 75, null, null, null, 25833162, 14319026, 18237724, 25260425, 47488, "SRX4041513", "SRS3258993", "SRA699717", "GEO", "Molecular Biology, Radboud University", 1, 0.68511, null, 0.1681, null, 0.87359, null, 0.50056, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-05-04", "Larval", "Larval", "Heart", "Cardiovascular System"], [48196, "SRR7119869", "SRX4041512", "SRS3258991", "SRP144601", "PRJNA459724", "The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis", "GSE114038", "Other", "Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively", null, "pubmed:30867528", null, "Danio rerio RNAseq singleHeart 3dpf mut 38", "GSM3131260", null, "tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2 / ", "Danio rerio RNAseq singleHeart 3dpf mut 38", "RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "heart", null, "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "Zebrafish Danio rerio  were housed at 27.5\u00b0C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.", "strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2 / ", "GSM3131260", "GSM3131260: Danio rerio RNAseq singleHeart 3dpf mut 38; Danio rerio; RNA Seq", "GSM3131260", null, "1", "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "GEO Accession:GSM3131260", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP144601", null, null, "NDCII_1_38_NDCII_sample_0038.fastq.gz", "fastq", 89200050.0, 1189334.0, "GSM3131260 r1", "0:75", "A:27880894;C:15422868;G:19386687;T:26456153;N:53448", 75, null, null, null, 27880894, 15422868, 19386687, 26456153, 53448, "SRX4041512", "SRS3258991", "SRA699717", "GEO", "Molecular Biology, Radboud University", 1, 0.63181, null, 0.17615, null, 0.86736, null, 0.5058, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-05-04", "Larval", "Larval", "Heart", "Cardiovascular System"], [48197, "SRR7119868", "SRX4041511", "SRS3258989", "SRP144601", "PRJNA459724", "The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis", "GSE114038", "Other", "Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively", null, "pubmed:30867528", null, "Danio rerio RNAseq singleHeart 3dpf mut 37", "GSM3131259", null, "tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2 / ", "Danio rerio RNAseq singleHeart 3dpf mut 37", "RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "heart", null, "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "Zebrafish Danio rerio  were housed at 27.5\u00b0C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.", "strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2 / ", "GSM3131259", "GSM3131259: Danio rerio RNAseq singleHeart 3dpf mut 37; Danio rerio; RNA Seq", "GSM3131259", null, "1", "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "GEO Accession:GSM3131259", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP144601", null, null, "NDCII_1_37_NDCII_sample_0037.fastq.gz", "fastq", 144136050.0, 1921814.0, "GSM3131259 r1", "0:75", "A:45236020;C:23884461;G:31356238;T:43570898;N:88433", 75, null, null, null, 45236020, 23884461, 31356238, 43570898, 88433, "SRX4041511", "SRS3258989", "SRA699717", "GEO", "Molecular Biology, Radboud University", 1, 0.64128, null, 0.19693, null, 0.86734, null, 0.54791, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-05-04", "Larval", "Larval", "Heart", "Cardiovascular System"], [48198, "SRR7119867", "SRX4041510", "SRS3258990", "SRP144601", "PRJNA459724", "The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis", "GSE114038", "Other", "Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively", null, "pubmed:30867528", null, "Danio rerio RNAseq singleHeart 3dpf mut 36", "GSM3131258", null, "tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2 / ", "Danio rerio RNAseq singleHeart 3dpf mut 36", "RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "heart", null, "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "Zebrafish Danio rerio  were housed at 27.5\u00b0C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.", "strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2 / ", "GSM3131258", "GSM3131258: Danio rerio RNAseq singleHeart 3dpf mut 36; Danio rerio; RNA Seq", "GSM3131258", null, "1", "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "GEO Accession:GSM3131258", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP144601", null, null, "NDCII_1_36_NDCII_sample_0036.fastq.gz", "fastq", 98485275.0, 1313137.0, "GSM3131258 r1", "0:75", "A:31078665;C:16821229;G:21507034;T:29019964;N:58383", 75, null, null, null, 31078665, 16821229, 21507034, 29019964, 58383, "SRX4041510", "SRS3258990", "SRA699717", "GEO", "Molecular Biology, Radboud University", 1, 0.62906, null, 0.24825, null, 0.86592, null, 0.56159, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-05-04", "Larval", "Larval", "Heart", "Cardiovascular System"], [48208, "SRR7119857", "SRX4041500", "SRS3258979", "SRP144601", "PRJNA459724", "The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis", "GSE114038", "Other", "Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively", null, "pubmed:30867528", null, "Danio rerio RNAseq singleHeart 3dpf wt 24", "GSM3131248", null, "tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2+/+", "Danio rerio RNAseq singleHeart 3dpf wt 24", "RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "heart", null, "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "Zebrafish Danio rerio  were housed at 27.5\u00b0C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.", "strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2+/+", "GSM3131248", "GSM3131248: Danio rerio RNAseq singleHeart 3dpf wt 24; Danio rerio; RNA Seq", "GSM3131248", null, "1", "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "GEO Accession:GSM3131248", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP144601", null, null, "NDCII_1_24_NDCII_sample_0024.fastq.gz", "fastq", 56268825.0, 750251.0, "GSM3131248 r1", "0:75", "A:17328594;C:9907009;G:12451765;T:16549368;N:32089", 75, null, null, null, 17328594, 9907009, 12451765, 16549368, 32089, "SRX4041500", "SRS3258979", "SRA699717", "GEO", "Molecular Biology, Radboud University", 1, 0.68698, null, 0.13156, null, 0.87647, null, 0.54659, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-05-04", "Larval", "Larval", "Heart", "Cardiovascular System"], [48209, "SRR7119856", "SRX4041499", "SRS3258978", "SRP144601", "PRJNA459724", "The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis", "GSE114038", "Other", "Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively", null, "pubmed:30867528", null, "Danio rerio RNAseq singleHeart 3dpf wt 23", "GSM3131247", null, "tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2+/+", "Danio rerio RNAseq singleHeart 3dpf wt 23", "RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "heart", null, "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "Zebrafish Danio rerio  were housed at 27.5\u00b0C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.", "strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2+/+", "GSM3131247", "GSM3131247: Danio rerio RNAseq singleHeart 3dpf wt 23; Danio rerio; RNA Seq", "GSM3131247", null, "1", "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "GEO Accession:GSM3131247", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP144601", null, null, "NDCII_1_23_NDCII_sample_0023.fastq.gz", "fastq", 113729700.0, 1516396.0, "GSM3131247 r1", "0:75", "A:34708329;C:19742375;G:24997702;T:34216965;N:64329", 75, null, null, null, 34708329, 19742375, 24997702, 34216965, 64329, "SRX4041499", "SRS3258978", "SRA699717", "GEO", "Molecular Biology, Radboud University", 1, 0.68965, null, 0.1358, null, 0.86168, null, 0.50041, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-05-04", "Larval", "Larval", "Heart", "Cardiovascular System"], [48210, "SRR7119855", "SRX4041498", "SRS3258976", "SRP144601", "PRJNA459724", "The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis", "GSE114038", "Other", "Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively", null, "pubmed:30867528", null, "Danio rerio RNAseq singleHeart 3dpf wt 22", "GSM3131246", null, "tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2+/+", "Danio rerio RNAseq singleHeart 3dpf wt 22", "RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "heart", null, "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "Zebrafish Danio rerio  were housed at 27.5\u00b0C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.", "strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2+/+", "GSM3131246", "GSM3131246: Danio rerio RNAseq singleHeart 3dpf wt 22; Danio rerio; RNA Seq", "GSM3131246", null, "1", "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "GEO Accession:GSM3131246", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP144601", null, null, "NDCII_1_22_NDCII_sample_0022.fastq.gz", "fastq", 129788625.0, 1730515.0, "GSM3131246 r1", "0:75", "A:39826852;C:22345144;G:28340986;T:39198043;N:77600", 75, null, null, null, 39826852, 22345144, 28340986, 39198043, 77600, "SRX4041498", "SRS3258976", "SRA699717", "GEO", "Molecular Biology, Radboud University", 1, 0.68637, null, 0.19709, null, 0.85662, null, 0.52926, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-05-04", "Larval", "Larval", "Heart", "Cardiovascular System"], [48211, "SRR7119854", "SRX4041497", "SRS3258975", "SRP144601", "PRJNA459724", "The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis", "GSE114038", "Other", "Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively", null, "pubmed:30867528", null, "Danio rerio RNAseq singleHeart 3dpf wt 21", "GSM3131245", null, "tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2+/+", "Danio rerio RNAseq singleHeart 3dpf wt 21", "RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "heart", null, "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "Zebrafish Danio rerio  were housed at 27.5\u00b0C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.", "strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2+/+", "GSM3131245", "GSM3131245: Danio rerio RNAseq singleHeart 3dpf wt 21; Danio rerio; RNA Seq", "GSM3131245", null, "1", "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "GEO Accession:GSM3131245", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP144601", null, null, "NDCII_1_21_NDCII_sample_0021.fastq.gz", "fastq", 74830575.0, 997741.0, "GSM3131245 r1", "0:75", "A:23292108;C:12771005;G:16485526;T:22236863;N:45073", 75, null, null, null, 23292108, 12771005, 16485526, 22236863, 45073, "SRX4041497", "SRS3258975", "SRA699717", "GEO", "Molecular Biology, Radboud University", 1, 0.62409, null, 0.23647, null, 0.88398, null, 0.52649, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-05-04", "Larval", "Larval", "Heart", "Cardiovascular System"], [48212, "SRR7119853", "SRX4041496", "SRS3258974", "SRP144601", "PRJNA459724", "The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis", "GSE114038", "Other", "Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively", null, "pubmed:30867528", null, "Danio rerio RNAseq singleHeart 3dpf wt 20", "GSM3131244", null, "tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2+/+", "Danio rerio RNAseq singleHeart 3dpf wt 20", "RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "heart", null, "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "Zebrafish Danio rerio  were housed at 27.5\u00b0C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.", "strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2+/+", "GSM3131244", "GSM3131244: Danio rerio RNAseq singleHeart 3dpf wt 20; Danio rerio; RNA Seq", "GSM3131244", null, "1", "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "GEO Accession:GSM3131244", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP144601", null, null, "NDCII_1_20_NDCII_sample_0020.fastq.gz", "fastq", 83202075.0, 1109361.0, "GSM3131244 r1", "0:75", "A:26090654;C:14537361;G:18178302;T:24348215;N:47543", 75, null, null, null, 26090654, 14537361, 18178302, 24348215, 47543, "SRX4041496", "SRS3258974", "SRA699717", "GEO", "Molecular Biology, Radboud University", 1, 0.59091, null, 0.18382, null, 0.87274, null, 0.50189, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-05-04", "Larval", "Larval", "Heart", "Cardiovascular System"], [48213, "SRR7119852", "SRX4041495", "SRS3258973", "SRP144601", "PRJNA459724", "The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis", "GSE114038", "Other", "Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively", null, "pubmed:30867528", null, "Danio rerio RNAseq singleHeart 3dpf wt 19", "GSM3131243", null, "tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2+/+", "Danio rerio RNAseq singleHeart 3dpf wt 19", "RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "heart", null, "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "Zebrafish Danio rerio  were housed at 27.5\u00b0C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.", "strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2+/+", "GSM3131243", "GSM3131243: Danio rerio RNAseq singleHeart 3dpf wt 19; Danio rerio; RNA Seq", "GSM3131243", null, "1", "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "GEO Accession:GSM3131243", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP144601", null, null, "NDCII_1_19_NDCII_sample_0019.fastq.gz", "fastq", 61352025.0, 818027.0, "GSM3131243 r1", "0:75", "A:19173237;C:10426603;G:13570586;T:18144746;N:36853", 75, null, null, null, 19173237, 10426603, 13570586, 18144746, 36853, "SRX4041495", "SRS3258973", "SRA699717", "GEO", "Molecular Biology, Radboud University", 1, 0.64995, null, 0.19171, null, 0.87213, null, 0.54952, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-05-04", "Larval", "Larval", "Heart", "Cardiovascular System"], [48214, "SRR7119851", "SRX4041494", "SRS3258972", "SRP144601", "PRJNA459724", "The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis", "GSE114038", "Other", "Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively", null, "pubmed:30867528", null, "Danio rerio RNAseq singleHeart 3dpf wt 18", "GSM3131242", null, "tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2+/+", "Danio rerio RNAseq singleHeart 3dpf wt 18", "RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "heart", null, "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "Zebrafish Danio rerio  were housed at 27.5\u00b0C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.", "strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2+/+", "GSM3131242", "GSM3131242: Danio rerio RNAseq singleHeart 3dpf wt 18; Danio rerio; RNA Seq", "GSM3131242", null, "1", "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "GEO Accession:GSM3131242", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP144601", null, null, "NDCII_1_18_NDCII_sample_0018.fastq.gz", "fastq", 55114425.0, 734859.0, "GSM3131242 r1", "0:75", "A:17302961;C:9444084;G:12256958;T:16079162;N:31260", 75, null, null, null, 17302961, 9444084, 12256958, 16079162, 31260, "SRX4041494", "SRS3258972", "SRA699717", "GEO", "Molecular Biology, Radboud University", 1, 0.64027, null, 0.2383, null, 0.87903, null, 0.53857, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-05-04", "Larval", "Larval", "Heart", "Cardiovascular System"], [48215, "SRR7119850", "SRX4041493", "SRS3258971", "SRP144601", "PRJNA459724", "The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis", "GSE114038", "Other", "Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively", null, "pubmed:30867528", null, "Danio rerio RNAseq singleHeart 3dpf wt 17", "GSM3131241", null, "tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2+/+", "Danio rerio RNAseq singleHeart 3dpf wt 17", "RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "heart", null, "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "Zebrafish Danio rerio  were housed at 27.5\u00b0C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.", "strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2+/+", "GSM3131241", "GSM3131241: Danio rerio RNAseq singleHeart 3dpf wt 17; Danio rerio; RNA Seq", "GSM3131241", null, "1", "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "GEO Accession:GSM3131241", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP144601", null, null, "NDCII_1_17_NDCII_sample_0017.fastq.gz", "fastq", 54385575.0, 725141.0, "GSM3131241 r1", "0:75", "A:17178884;C:9154385;G:11956346;T:16062768;N:33192", 75, null, null, null, 17178884, 9154385, 11956346, 16062768, 33192, "SRX4041493", "SRS3258971", "SRA699717", "GEO", "Molecular Biology, Radboud University", 1, 0.6122, null, 0.27421, null, 0.88552, null, 0.5705, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-05-04", "Larval", "Larval", "Heart", "Cardiovascular System"], [48216, "SRR7119849", "SRX4041492", "SRS3258970", "SRP144601", "PRJNA459724", "The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis", "GSE114038", "Other", "Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively", null, "pubmed:30867528", null, "Danio rerio RNAseq singleHeart 3dpf wt 16", "GSM3131240", null, "tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2+/+", "Danio rerio RNAseq singleHeart 3dpf wt 16", "RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "heart", null, "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "Zebrafish Danio rerio  were housed at 27.5\u00b0C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.", "strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2+/+", "GSM3131240", "GSM3131240: Danio rerio RNAseq singleHeart 3dpf wt 16; Danio rerio; RNA Seq", "GSM3131240", null, "1", "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "GEO Accession:GSM3131240", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP144601", null, null, "NDCII_1_16_NDCII_sample_0016.fastq.gz", "fastq", 68361225.0, 911483.0, "GSM3131240 r1", "0:75", "A:20763268;C:11958924;G:16351810;T:19246084;N:41139", 75, null, null, null, 20763268, 11958924, 16351810, 19246084, 41139, "SRX4041492", "SRS3258970", "SRA699717", "GEO", "Molecular Biology, Radboud University", 1, 0.64264, null, 0.12251, null, 0.88477, null, 0.57059, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-05-04", "Larval", "Larval", "Heart", "Cardiovascular System"], [48217, "SRR7119848", "SRX4041491", "SRS3258969", "SRP144601", "PRJNA459724", "The Polycomb Group protein Rnf2/Ring1b is essential for zebrafish development and cardiogenesis", "GSE114038", "Other", "Goal of the experiment was to assess the differences in gene expression between zygotic rnf2 mutant zebrafish embryos and wildtype embryos at 3 dpf. The goal of ChIP sequencing of wildtype embryos at 3 dpf is to link deregulation in gene expression to the Rnf2 occupancy in the wildtype situation and check the overlap between Rnf2 and H3K27me3. The RNA sequencing of single hearts was performed to assess differences in gene expression between zygotic rn2 mutants hearts and wildtype hearts at 3 different stages 1  2  3 dpf Overall design: RNAseq of 3dpf Danio rerio whole embyos  wild types and rnf2 mutants 8 and 7 replicates  respectively; ChIPseq for rnf2 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in;  ChIPseq for H327me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 2 replicates embryos; ChIPseq for H3K27me3 in 3dpf Danio rerio wild type 2 replicates and rnf2 mutant 1 sample embryos all 3 with Drosophila spike in; RNAseq of 1  2 dpf and 3 dpf Danio rerio dissected hearts  wild types 9  13 and 10 replicates  respectively and rnf2 mutants 8  9 and 9 replicates  respectively", null, "pubmed:30867528", null, "Danio rerio RNAseq singleHeart 3dpf wt 15", "GSM3131239", null, "tissue:heart|strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2+/+", "Danio rerio RNAseq singleHeart 3dpf wt 15", "RNA seq reads from whole embryos were mapped to genome GRCz10 + transcriptome v87 from ensembl using STAR version 2.5.2b with   quantMode geneCounts Batch effect was removed with R package RUVseq version 1.10.0 obtaining final normalized counts with DESeq2 version 1.16.1 ChIPseq reads were aligned to the genome GRCz10 using bwa version 0.7.15 with default parameters Aligned reads were further processed removing multimappers and duplicated reads using Picard MarkDuplicates 2.8.2 ChIP seq peaks were called using macs2 version 2.1.1 with qvalue cutoff=1e 02 relative to respective ChIP input track. RNAseq reads from dissected hearts were demultiplexed and processed following the CEL Seq pipeline https://github.com/yanailab/CEL Seq pipeline Normalized counts were obtained with Monocle version 2.4.0 Genome build: GRCz10 Supplementary files format and content: Gene counts .txt; peak files in BED format", "heart", null, "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "Zebrafish Danio rerio  were housed at 27.5\u00b0C in a 14/10h light/dark cycle. The evening before spawning  one male and one female were placed into a tank with a divider and merged the following morning. Spontaneous spawning occurred when the male and female were put together at the moment the light turned on. Embryos were collected and staged according to Kimmel et al. Kimmel et al.  1995.", "strain:TU/TLF mixed background|cell type:heart|age:3dpf|genotype:myl7:GFP rnf2+/+", "GSM3131239", "GSM3131239: Danio rerio RNAseq singleHeart 3dpf wt 15; Danio rerio; RNA Seq", "GSM3131239", null, "1", "RNA seq: Embryos of 3 dpf were homogenized in TRIzol and the ZYMO RNA microprep kit was used to isolate RNA and treat the samples with DNAseI. rRNA was depleted using the illumina RiboZero kit RNA seq: extraction was followed by fragmentation  cDNA synthesis  and KAPA HYPERprep library preparation", "GEO Accession:GSM3131239", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP144601", null, null, "NDCII_1_15_NDCII_sample_0015.fastq.gz", "fastq", 43246350.0, 576618.0, "GSM3131239 r1", "0:75", "A:13423239;C:7409151;G:9733956;T:12657584;N:22420", 75, null, null, null, 13423239, 7409151, 9733956, 12657584, 22420, "SRX4041491", "SRS3258969", "SRA699717", "GEO", "Molecular Biology, Radboud University", 1, 0.66495, null, 0.14227, null, 0.88828, null, 0.56869, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "rrna_depletion", "ribozero", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2018-05-04", "Larval", "Larval", "Heart", "Cardiovascular System"], [49850, "SRR8883829", "SRX5669659", "SRS4612528", "SRP166782", "PRJNA498309", "Functional heterogeneity within the developing zebrafish epicardium", "GSE121750", "Transcriptome Analysis", "The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells", null, "pubmed:32084358", null, "148 2 E12 KOcxcl12a 6 reseq", "GSM3719057", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "148 2 E12 KOcxcl12a 6 reseq", "Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC", "Heart", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719057", "GSM3719057: 148 2 E12 KOcxcl12a 6 reseq; Danio rerio; RNA Seq", "GSM3719057", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719057", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "148-2-E12-KOcxcl12a-6_reseq_all_lanes_R1.fastq.gz", "fastq", 763065205.0, 10372479.0, "GSM3719057 r1", "0:73.57 1:0", "A:179985921;C:199425581;G:205920814;T:177110327;N:622562", 73, 0, null, null, 179985921, 199425581, 205920814, 177110327, 622562, "SRX5669659", "SRS4612528", "SRA798477", "GEO", "University of Oxford", 1, 0.93161, null, 0.2297, null, 0.75684, null, 0.64613, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49851, "SRR8883828", "SRX5669658", "SRS4612527", "SRP166782", "PRJNA498309", "Functional heterogeneity within the developing zebrafish epicardium", "GSE121750", "Transcriptome Analysis", "The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells", null, "pubmed:32084358", null, "147 2 E11 KOcxcl12a 5 reseq", "GSM3719056", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "147 2 E11 KOcxcl12a 5 reseq", "Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC", "Heart", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719056", "GSM3719056: 147 2 E11 KOcxcl12a 5 reseq; Danio rerio; RNA Seq", "GSM3719056", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719056", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "147-2-E11-KOcxcl12a-5_reseq_all_lanes_R1.fastq.gz", "fastq", 777154556.0, 10544824.0, "GSM3719056 r1", "0:73.70 1:0", "A:182318789;C:204282719;G:210781481;T:179272833;N:498734", 73, 0, null, null, 182318789, 204282719, 210781481, 179272833, 498734, "SRX5669658", "SRS4612527", "SRA798477", "GEO", "University of Oxford", 1, 0.94256, null, 0.25229, null, 0.76781, null, 0.67336, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49852, "SRR8883827", "SRX5669657", "SRS4612526", "SRP166782", "PRJNA498309", "Functional heterogeneity within the developing zebrafish epicardium", "GSE121750", "Transcriptome Analysis", "The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells", null, "pubmed:32084358", null, "146 2 E10 KOcxcl12a 4 reseq", "GSM3719055", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "146 2 E10 KOcxcl12a 4 reseq", "Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC", "Heart", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719055", "GSM3719055: 146 2 E10 KOcxcl12a 4 reseq; Danio rerio; RNA Seq", "GSM3719055", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719055", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "146-2-E10-KOcxcl12a-4_reseq_all_lanes_R1.fastq.gz", "fastq", 893756036.0, 12231836.0, "GSM3719055 r1", "0:73.07 1:0", "A:208987215;C:235365706;G:243090724;T:205234077;N:1078314", 73, 0, null, null, 208987215, 235365706, 243090724, 205234077, 1078314, "SRX5669657", "SRS4612526", "SRA798477", "GEO", "University of Oxford", 1, 0.93675, null, 0.21776, null, 0.76597, null, 0.63391, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49853, "SRR8883826", "SRX5669656", "SRS4612525", "SRP166782", "PRJNA498309", "Functional heterogeneity within the developing zebrafish epicardium", "GSE121750", "Transcriptome Analysis", "The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells", null, "pubmed:32084358", null, "145 2 E09 KOcxcl12a 3 reseq", "GSM3719054", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "145 2 E09 KOcxcl12a 3 reseq", "Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC", "Heart", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719054", "GSM3719054: 145 2 E09 KOcxcl12a 3 reseq; Danio rerio; RNA Seq", "GSM3719054", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719054", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "145-2-E09-KOcxcl12a-3_reseq_all_lanes_R1.fastq.gz", "fastq", 850857048.0, 11668488.0, "GSM3719054 r1", "0:72.92 1:0", "A:205769666;C:217594988;G:223805195;T:202463052;N:1224147", 72, 0, null, null, 205769666, 217594988, 223805195, 202463052, 1224147, "SRX5669656", "SRS4612525", "SRA798477", "GEO", "University of Oxford", 1, 0.92738, null, 0.2566, null, 0.75152, null, 0.65144, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49854, "SRR8883825", "SRX5669655", "SRS4612524", "SRP166782", "PRJNA498309", "Functional heterogeneity within the developing zebrafish epicardium", "GSE121750", "Transcriptome Analysis", "The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells", null, "pubmed:32084358", null, "144 2 E08 KOcxcl12a 2 reseq", "GSM3719053", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "144 2 E08 KOcxcl12a 2 reseq", "Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC", "Heart", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719053", "GSM3719053: 144 2 E08 KOcxcl12a 2 reseq; Danio rerio; RNA Seq", "GSM3719053", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719053", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "144-2-E08-KOcxcl12a-2_reseq_all_lanes_R1.fastq.gz", "fastq", 898577334.0, 12271421.0, "GSM3719053 r1", "0:73.23 1:0", "A:209765901;C:237376777;G:244548553;T:205953258;N:932845", 73, 0, null, null, 209765901, 237376777, 244548553, 205953258, 932845, "SRX5669655", "SRS4612524", "SRA798477", "GEO", "University of Oxford", 1, 0.94312, null, 0.22115, null, 0.75751, null, 0.63782, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49855, "SRR8883824", "SRX5669654", "SRS4612523", "SRP166782", "PRJNA498309", "Functional heterogeneity within the developing zebrafish epicardium", "GSE121750", "Transcriptome Analysis", "The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells", null, "pubmed:32084358", null, "143 2 E07 KOcxcl12a 1 reseq", "GSM3719052", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "143 2 E07 KOcxcl12a 1 reseq", "Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC", "Heart", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719052", "GSM3719052: 143 2 E07 KOcxcl12a 1 reseq; Danio rerio; RNA Seq", "GSM3719052", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719052", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "143-2-E07-KOcxcl12a-1_reseq_all_lanes_R1.fastq.gz", "fastq", 642191206.0, 8724687.0, "GSM3719052 r1", "0:73.61 1:0", "A:148702964;C:170638392;G:176459501;T:145895525;N:494824", 73, 0, null, null, 148702964, 170638392, 176459501, 145895525, 494824, "SRX5669654", "SRS4612523", "SRA798477", "GEO", "University of Oxford", 1, 0.93805, null, 0.20319, null, 0.76203, null, 0.65533, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49856, "SRR8883823", "SRX5669653", "SRS4612522", "SRP166782", "PRJNA498309", "Functional heterogeneity within the developing zebrafish epicardium", "GSE121750", "Transcriptome Analysis", "The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells", null, "pubmed:32084358", null, "142 2 E06 KOcxcl12a ctr 3 reseq", "GSM3719051", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "142 2 E06 KOcxcl12a ctr 3 reseq", "Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC", "Heart", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719051", "GSM3719051: 142 2 E06 KOcxcl12a ctr 3 reseq; Danio rerio; RNA Seq", "GSM3719051", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719051", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "142-2-E06-KOcxcl12a-ctr-3_reseq_all_lanes_R1.fastq.gz", "fastq", 913646709.0, 12532356.0, "GSM3719051 r1", "0:72.90 1:0", "A:210664396;C:243042644;G:251444631;T:207071337;N:1423701", 72, 0, null, null, 210664396, 243042644, 251444631, 207071337, 1423701, "SRX5669653", "SRS4612522", "SRA798477", "GEO", "University of Oxford", 1, 0.93582, null, 0.21132, null, 0.7669, null, 0.65882, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49857, "SRR8883822", "SRX5669652", "SRS4612521", "SRP166782", "PRJNA498309", "Functional heterogeneity within the developing zebrafish epicardium", "GSE121750", "Transcriptome Analysis", "The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells", null, "pubmed:32084358", null, "141 2 E05 KOcxcl12a ctr 2 reseq", "GSM3719050", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "141 2 E05 KOcxcl12a ctr 2 reseq", "Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC", "Heart", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719050", "GSM3719050: 141 2 E05 KOcxcl12a ctr 2 reseq; Danio rerio; RNA Seq", "GSM3719050", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719050", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "141-2-E05-KOcxcl12a-ctr-2_reseq_all_lanes_R1.fastq.gz", "fastq", 698256933.0, 9557079.0, "GSM3719050 r1", "0:73.06 1:0", "A:165636445;C:181576831;G:187431558;T:162693862;N:918237", 73, 0, null, null, 165636445, 181576831, 187431558, 162693862, 918237, "SRX5669652", "SRS4612521", "SRA798477", "GEO", "University of Oxford", 1, 0.92623, null, 0.20301, null, 0.75562, null, 0.58643, null, 74, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49858, "SRR8883821", "SRX5669651", "SRS4612520", "SRP166782", "PRJNA498309", "Functional heterogeneity within the developing zebrafish epicardium", "GSE121750", "Transcriptome Analysis", "The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells", null, "pubmed:32084358", null, "140 2 E04 KOcxcl12a ctr 1 reseq", "GSM3719049", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "140 2 E04 KOcxcl12a ctr 1 reseq", "Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC", "Heart", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719049", "GSM3719049: 140 2 E04 KOcxcl12a ctr 1 reseq; Danio rerio; RNA Seq", "GSM3719049", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719049", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "140-2-E04-KOcxcl12a-ctr-1_reseq_all_lanes_R1.fastq.gz", "fastq", 824049635.0, 11240750.0, "GSM3719049 r1", "0:73.31 1:0", "A:195127513;C:214512790;G:222034432;T:191506323;N:868577", 73, 0, null, null, 195127513, 214512790, 222034432, 191506323, 868577, "SRX5669651", "SRS4612520", "SRA798477", "GEO", "University of Oxford", 1, 0.93289, null, 0.20393, null, 0.75749, null, 0.60814, null, 74, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49859, "SRR8883820", "SRX5669650", "SRS4612519", "SRP166782", "PRJNA498309", "Functional heterogeneity within the developing zebrafish epicardium", "GSE121750", "Transcriptome Analysis", "The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells", null, "pubmed:32084358", null, "130 2 D06 KOsema3fb tbx18 1 reseq", "GSM3719048", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "130 2 D06 KOsema3fb tbx18 1 reseq", "Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC", "Heart", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719048", "GSM3719048: 130 2 D06 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq", "GSM3719048", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719048", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "130-2-D06-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 1162709924.0, 15925191.0, "GSM3719048 r1", "0:73.01 1:0", "A:289120225;C:287784856;G:301546291;T:282206243;N:2052309", 73, 0, null, null, 289120225, 287784856, 301546291, 282206243, 2052309, "SRX5669650", "SRS4612519", "SRA798477", "GEO", "University of Oxford", 1, 0.7653, null, 0.25001, null, 0.98997, null, 0.83422, null, 74, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49860, "SRR8883819", "SRX5669649", "SRS4612518", "SRP166782", "PRJNA498309", "Functional heterogeneity within the developing zebrafish epicardium", "GSE121750", "Transcriptome Analysis", "The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells", null, "pubmed:32084358", null, "124 2 C12 KOsema3fb tbx18 1 reseq", "GSM3719047", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "124 2 C12 KOsema3fb tbx18 1 reseq", "Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC", "Heart", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719047", "GSM3719047: 124 2 C12 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq", "GSM3719047", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719047", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "124-2-C12-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 299825780.0, 4022960.0, "GSM3719047 r1", "0:74.53 1:0", "A:68392314;C:78125239;G:84196045;T:69093198;N:18984", 74, 0, null, null, 68392314, 78125239, 84196045, 69093198, 18984, "SRX5669649", "SRS4612518", "SRA798477", "GEO", "University of Oxford", 1, 0.74846, null, 0.27048, null, 0.99557, null, 0.70087, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49861, "SRR8883818", "SRX5669648", "SRS4612517", "SRP166782", "PRJNA498309", "Functional heterogeneity within the developing zebrafish epicardium", "GSE121750", "Transcriptome Analysis", "The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells", null, "pubmed:32084358", null, "123 2 C11 KOsema3fb tbx18 1 reseq", "GSM3719046", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "123 2 C11 KOsema3fb tbx18 1 reseq", "Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC", "Heart", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719046", "GSM3719046: 123 2 C11 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq", "GSM3719046", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719046", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "123-2-C11-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 295959651.0, 3971786.0, "GSM3719046 r1", "0:74.52 1:0", "A:77279704;C:70402673;G:74373147;T:73882710;N:21417", 74, 0, null, null, 77279704, 70402673, 74373147, 73882710, 21417, "SRX5669648", "SRS4612517", "SRA798477", "GEO", "University of Oxford", 1, 0.82981, null, 0.14333, null, 0.99758, null, 0.91205, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49862, "SRR8883817", "SRX5669647", "SRS4612516", "SRP166782", "PRJNA498309", "Functional heterogeneity within the developing zebrafish epicardium", "GSE121750", "Transcriptome Analysis", "The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells", null, "pubmed:32084358", null, "119 2 C07 KOsema3fb tbx18 1 reseq", "GSM3719045", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "119 2 C07 KOsema3fb tbx18 1 reseq", "Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC", "Heart", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719045", "GSM3719045: 119 2 C07 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq", "GSM3719045", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719045", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "119-2-C07-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 264496882.0, 3548156.0, "GSM3719045 r1", "0:74.54 1:0", "A:75579264;C:55698110;G:58441353;T:74755905;N:22250", 74, 0, null, null, 75579264, 55698110, 58441353, 74755905, 22250, "SRX5669647", "SRS4612516", "SRA798477", "GEO", "University of Oxford", 1, 0.80888, null, 0.37987, null, 0.98039, null, 0.91771, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49863, "SRR8883816", "SRX5669646", "SRS4612515", "SRP166782", "PRJNA498309", "Functional heterogeneity within the developing zebrafish epicardium", "GSE121750", "Transcriptome Analysis", "The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells", null, "pubmed:32084358", null, "113 2 C01 KOsema3fb tbx18 1 reseq", "GSM3719044", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "113 2 C01 KOsema3fb tbx18 1 reseq", "Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC", "Heart", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719044", "GSM3719044: 113 2 C01 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq", "GSM3719044", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719044", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "113-2-C01-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 900078149.0, 12264833.0, "GSM3719044 r1", "0:73.39 1:0", "A:219770321;C:225774705;G:235824823;T:217584908;N:1123392", 73, 0, null, null, 219770321, 225774705, 235824823, 217584908, 1123392, "SRX5669646", "SRS4612515", "SRA798477", "GEO", "University of Oxford", 1, 0.7672, null, 0.32569, null, 0.9811, null, 0.69383, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49864, "SRR8883815", "SRX5669645", "SRS4612514", "SRP166782", "PRJNA498309", "Functional heterogeneity within the developing zebrafish epicardium", "GSE121750", "Transcriptome Analysis", "The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells", null, "pubmed:32084358", null, "109 2 B08 KOsema3fb tbx18 1 reseq", "GSM3719043", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "109 2 B08 KOsema3fb tbx18 1 reseq", "Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC", "Heart", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719043", "GSM3719043: 109 2 B08 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq", "GSM3719043", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719043", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "109-2-B08-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 1184134969.0, 16001572.0, "GSM3719043 r1", "0:74.00 1:0", "A:349230233;C:244528650;G:253057471;T:336773385;N:545230", 74, 0, null, null, 349230233, 244528650, 253057471, 336773385, 545230, "SRX5669645", "SRS4612514", "SRA798477", "GEO", "University of Oxford", 1, 0.88887, null, 0.09304, null, 0.99348, null, 0.98604, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49865, "SRR8883814", "SRX5669644", "SRS4612513", "SRP166782", "PRJNA498309", "Functional heterogeneity within the developing zebrafish epicardium", "GSE121750", "Transcriptome Analysis", "The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells", null, "pubmed:32084358", null, "106 2 B05 KOsema3fb tbx18 1 reseq", "GSM3719042", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "106 2 B05 KOsema3fb tbx18 1 reseq", "Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC", "Heart", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719042", "GSM3719042: 106 2 B05 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq", "GSM3719042", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719042", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "106-2-B05-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 1419090881.0, 19189635.0, "GSM3719042 r1", "0:73.95 1:0", "A:373650546;C:329135514;G:344779857;T:370771195;N:753769", 73, 0, null, null, 373650546, 329135514, 344779857, 370771195, 753769, "SRX5669644", "SRS4612513", "SRA798477", "GEO", "University of Oxford", 1, 0.80666, null, 0.39497, null, 0.98307, null, 0.82884, null, 74, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49866, "SRR8883813", "SRX5669643", "SRS4612512", "SRP166782", "PRJNA498309", "Functional heterogeneity within the developing zebrafish epicardium", "GSE121750", "Transcriptome Analysis", "The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells", null, "pubmed:32084358", null, "102 2 B01 KOsema3fb tbx18 1 reseq", "GSM3719041", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "102 2 B01 KOsema3fb tbx18 1 reseq", "Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC", "Heart", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719041", "GSM3719041: 102 2 B01 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq", "GSM3719041", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719041", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "102-2-B01-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 792286694.0, 10728522.0, "GSM3719041 r1", "0:73.85 1:0", "A:208005708;C:185723186;G:192254855;T:205724930;N:578015", 73, 0, null, null, 208005708, 185723186, 192254855, 205724930, 578015, "SRX5669643", "SRS4612512", "SRA798477", "GEO", "University of Oxford", 1, 0.83885, null, 0.20822, null, 0.93385, null, 0.55626, null, 74, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49867, "SRR8883812", "SRX5669642", "SRS4612511", "SRP166782", "PRJNA498309", "Functional heterogeneity within the developing zebrafish epicardium", "GSE121750", "Transcriptome Analysis", "The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells", null, "pubmed:32084358", null, "099 2 A10 KOsema3fb tbx18 1 reseq", "GSM3719040", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "099 2 A10 KOsema3fb tbx18 1 reseq", "Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC", "Heart", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719040", "GSM3719040: 099 2 A10 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq", "GSM3719040", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719040", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "099-2-A10-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 1259856601.0, 17276596.0, "GSM3719040 r1", "0:72.92 1:0", "A:327815757;C:292688430;G:309183926;T:327561592;N:2606896", 72, 0, null, null, 327815757, 292688430, 309183926, 327561592, 2606896, "SRX5669642", "SRS4612511", "SRA798477", "GEO", "University of Oxford", 1, 0.75716, null, 0.21591, null, 0.98545, null, 0.88552, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49868, "SRR8883811", "SRX5669641", "SRS4612510", "SRP166782", "PRJNA498309", "Functional heterogeneity within the developing zebrafish epicardium", "GSE121750", "Transcriptome Analysis", "The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells", null, "pubmed:32084358", null, "094 2 A04 KOsema3fb tbx18 1 reseq", "GSM3719039", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "094 2 A04 KOsema3fb tbx18 1 reseq", "Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC", "Heart", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719039", "GSM3719039: 094 2 A04 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq", "GSM3719039", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719039", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "094-2-A04-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 1393707010.0, 19037650.0, "GSM3719039 r1", "0:73.21 1:0", "A:419699742;C:277700843;G:287769215;T:406877217;N:1659993", 73, 0, null, null, 419699742, 277700843, 287769215, 406877217, 1659993, "SRX5669641", "SRS4612510", "SRA798477", "GEO", "University of Oxford", 1, 0.89441, null, 0.12858, null, 0.98875, null, 0.97807, null, 74, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49869, "SRR8883810", "SRX5669640", "SRS4612509", "SRP166782", "PRJNA498309", "Functional heterogeneity within the developing zebrafish epicardium", "GSE121750", "Transcriptome Analysis", "The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells", null, "pubmed:32084358", null, "091 2 A01 KOsema3fb tbx18 1 reseq", "GSM3719038", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "091 2 A01 KOsema3fb tbx18 1 reseq", "Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC", "Heart", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719038", "GSM3719038: 091 2 A01 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq", "GSM3719038", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719038", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "091-2-A01-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 1312071784.0, 17781006.0, "GSM3719038 r1", "0:73.79 1:0", "A:366473328;C:287833987;G:300280345;T:356559257;N:924867", 73, 0, null, null, 366473328, 287833987, 300280345, 356559257, 924867, "SRX5669640", "SRS4612509", "SRA798477", "GEO", "University of Oxford", 1, 0.84829, null, 0.13012, null, 0.99239, null, 0.95627, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49870, "SRR8883809", "SRX5669639", "SRS4612508", "SRP166782", "PRJNA498309", "Functional heterogeneity within the developing zebrafish epicardium", "GSE121750", "Transcriptome Analysis", "The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells", null, "pubmed:32084358", null, "089 1 H11 KOsema3fb tbx18 1 reseq", "GSM3719037", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "089 1 H11 KOsema3fb tbx18 1 reseq", "Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC", "Heart", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719037", "GSM3719037: 089 1 H11 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq", "GSM3719037", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719037", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "089-1-H11-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 457617610.0, 6259652.0, "GSM3719037 r1", "0:73.11 1:0", "A:102784836;C:123244653;G:128352318;T:102443570;N:792233", 73, 0, null, null, 102784836, 123244653, 128352318, 102443570, 792233, "SRX5669639", "SRS4612508", "SRA798477", "GEO", "University of Oxford", 1, 0.41215, null, 0.14696, null, 0.99474, null, 0.79701, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49871, "SRR8883808", "SRX5669638", "SRS4612507", "SRP166782", "PRJNA498309", "Functional heterogeneity within the developing zebrafish epicardium", "GSE121750", "Transcriptome Analysis", "The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells", null, "pubmed:32084358", null, "088 1 H10 KOsema3fb tbx18 1 reseq", "GSM3719036", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "088 1 H10 KOsema3fb tbx18 1 reseq", "Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC", "Heart", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719036", "GSM3719036: 088 1 H10 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq", "GSM3719036", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719036", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "088-1-H10-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 1045203718.0, 14235004.0, "GSM3719036 r1", "0:73.42 1:0", "A:245506754;C:275986612;G:284480834;T:238462022;N:767496", 73, 0, null, null, 245506754, 275986612, 284480834, 238462022, 767496, "SRX5669638", "SRS4612507", "SRA798477", "GEO", "University of Oxford", 1, 0.78399, null, 0.27279, null, 0.96171, null, 0.64393, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49872, "SRR8883807", "SRX5669637", "SRS4612506", "SRP166782", "PRJNA498309", "Functional heterogeneity within the developing zebrafish epicardium", "GSE121750", "Transcriptome Analysis", "The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells", null, "pubmed:32084358", null, "085 1 H07 KOsema3fb tbx18 1 reseq", "GSM3719035", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "085 1 H07 KOsema3fb tbx18 1 reseq", "Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC", "Heart", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719035", "GSM3719035: 085 1 H07 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq", "GSM3719035", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719035", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "085-1-H07-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 994545532.0, 13515281.0, "GSM3719035 r1", "0:73.59 1:0", "A:251733790;C:239766112;G:249497960;T:252514979;N:1032691", 73, 0, null, null, 251733790, 239766112, 249497960, 252514979, 1032691, "SRX5669637", "SRS4612506", "SRA798477", "GEO", "University of Oxford", 1, 0.76592, null, 0.33384, null, 0.97488, null, 0.6386, null, 74, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49873, "SRR8883806", "SRX5669636", "SRS4612505", "SRP166782", "PRJNA498309", "Functional heterogeneity within the developing zebrafish epicardium", "GSE121750", "Transcriptome Analysis", "The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells", null, "pubmed:32084358", null, "083 1 H05 KOsema3fb tbx18 1 reseq", "GSM3719034", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "083 1 H05 KOsema3fb tbx18 1 reseq", "Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC", "Heart", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719034", "GSM3719034: 083 1 H05 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq", "GSM3719034", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719034", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "083-1-H05-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 1559012386.0, 21214346.0, "GSM3719034 r1", "0:73.49 1:0", "A:377233697;C:392858147;G:413542175;T:373251234;N:2127133", 73, 0, null, null, 377233697, 392858147, 413542175, 373251234, 2127133, "SRX5669636", "SRS4612505", "SRA798477", "GEO", "University of Oxford", 1, 0.76884, null, 0.25038, null, 0.99304, null, 0.82504, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49874, "SRR8883805", "SRX5669635", "SRS4612504", "SRP166782", "PRJNA498309", "Functional heterogeneity within the developing zebrafish epicardium", "GSE121750", "Transcriptome Analysis", "The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells", null, "pubmed:32084358", null, "080 1 H02 KOsema3fb tbx18 1 reseq", "GSM3719033", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "080 1 H02 KOsema3fb tbx18 1 reseq", "Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC", "Heart", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719033", "GSM3719033: 080 1 H02 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq", "GSM3719033", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719033", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "080-1-H02-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 1858691358.0, 25414284.0, "GSM3719033 r1", "0:73.14 1:0", "A:476963365;C:445987754;G:466752717;T:466112688;N:2874834", 73, 0, null, null, 476963365, 445987754, 466752717, 466112688, 2874834, "SRX5669635", "SRS4612504", "SRA798477", "GEO", "University of Oxford", 1, 0.68992, null, 0.2736, null, 0.982, null, 0.82915, null, 59, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49875, "SRR8883804", "SRX5669634", "SRS4612503", "SRP166782", "PRJNA498309", "Functional heterogeneity within the developing zebrafish epicardium", "GSE121750", "Transcriptome Analysis", "The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells", null, "pubmed:32084358", null, "075 1 G09 KOsema3fb tbx18 1 reseq", "GSM3719032", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "075 1 G09 KOsema3fb tbx18 1 reseq", "Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC", "Heart", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719032", "GSM3719032: 075 1 G09 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq", "GSM3719032", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719032", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "075-1-G09-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 268112375.0, 3598019.0, "GSM3719032 r1", "0:74.52 1:0", "A:65372074;C:67071915;G:71029798;T:64617919;N:20669", 74, 0, null, null, 65372074, 67071915, 71029798, 64617919, 20669, "SRX5669634", "SRS4612503", "SRA798477", "GEO", "University of Oxford", 1, 0.67884, null, 0.23576, null, 0.98717, null, 0.82171, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49876, "SRR8883803", "SRX5669633", "SRS4612502", "SRP166782", "PRJNA498309", "Functional heterogeneity within the developing zebrafish epicardium", "GSE121750", "Transcriptome Analysis", "The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells", null, "pubmed:32084358", null, "071 1 G05 KOsema3fb tbx18 1 reseq", "GSM3719031", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "071 1 G05 KOsema3fb tbx18 1 reseq", "Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC", "Heart", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719031", "GSM3719031: 071 1 G05 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq", "GSM3719031", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719031", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "071-1-G05-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 828746401.0, 11302582.0, "GSM3719031 r1", "0:73.32 1:0", "A:229221425;C:183717145;G:190544172;T:224163771;N:1099888", 73, 0, null, null, 229221425, 183717145, 190544172, 224163771, 1099888, "SRX5669633", "SRS4612502", "SRA798477", "GEO", "University of Oxford", 1, 0.81759, null, 0.13538, null, 0.89315, null, 0.45516, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49877, "SRR8883802", "SRX5669631", "SRS4612500", "SRP166782", "PRJNA498309", "Functional heterogeneity within the developing zebrafish epicardium", "GSE121750", "Transcriptome Analysis", "The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells", null, "pubmed:32084358", null, "070 1 G04 KOsema3fb tbx18 1 reseq", "GSM3719030", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "070 1 G04 KOsema3fb tbx18 1 reseq", "Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC", "Heart", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719030", "GSM3719030: 070 1 G04 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq", "GSM3719030", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719030", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "070-1-G04-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 106414765.0, 1428334.0, "GSM3719030 r1", "0:74.50 1:0", "A:29193564;C:23683625;G:26548630;T:26978197;N:10749", 74, 0, null, null, 29193564, 23683625, 26548630, 26978197, 10749, "SRX5669631", "SRS4612500", "SRA798477", "GEO", "University of Oxford", 1, 0.4816, null, 0.11056, null, 0.99176, null, 0.92847, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49878, "SRR8883801", "SRX5669630", "SRS4612499", "SRP166782", "PRJNA498309", "Functional heterogeneity within the developing zebrafish epicardium", "GSE121750", "Transcriptome Analysis", "The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells", null, "pubmed:32084358", null, "063 1 F09 KOsema3fb tbx18 1 reseq", "GSM3719029", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "063 1 F09 KOsema3fb tbx18 1 reseq", "Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC", "Heart", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719029", "GSM3719029: 063 1 F09 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq", "GSM3719029", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719029", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "063-1-F09-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 1418543217.0, 19449719.0, "GSM3719029 r1", "0:72.93 1:0", "A:337365498;C:374610477;G:384311752;T:320594026;N:1661464", 72, 0, null, null, 337365498, 374610477, 384311752, 320594026, 1661464, "SRX5669630", "SRS4612499", "SRA798477", "GEO", "University of Oxford", 1, 0.72075, null, 0.19017, null, 0.94852, null, 0.65802, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49879, "SRR8883800", "SRX5669629", "SRS4612498", "SRP166782", "PRJNA498309", "Functional heterogeneity within the developing zebrafish epicardium", "GSE121750", "Transcriptome Analysis", "The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells", null, "pubmed:32084358", null, "059 1 F05 KOsema3fb tbx18 1 reseq", "GSM3719028", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "059 1 F05 KOsema3fb tbx18 1 reseq", "Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC", "Heart", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719028", "GSM3719028: 059 1 F05 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq", "GSM3719028", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719028", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "059-1-F05-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 628014958.0, 8461681.0, "GSM3719028 r1", "0:74.22 1:0", "A:169712705;C:143325768;G:146633959;T:168144033;N:198493", 74, 0, null, null, 169712705, 143325768, 146633959, 168144033, 198493, "SRX5669629", "SRS4612498", "SRA798477", "GEO", "University of Oxford", 1, 0.88635, null, 0.30859, null, 0.94945, null, 0.51713, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"], [49880, "SRR8883799", "SRX5669628", "SRS4612497", "SRP166782", "PRJNA498309", "Functional heterogeneity within the developing zebrafish epicardium", "GSE121750", "Transcriptome Analysis", "The epicardium is essential during cardiac development  homeostasis and repair and yet fundamental insights into its underlying cell biology  notably epicardium formation  lineage heterogeneity and functional cross talk with other cell types in the heart  is currently lacking. In this study  we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programmes and distinctive spatial distribution within the developing heart. Perturbation of unique gene signatures uncovered distinct functions associated with each subpopulation and established novel epicardial roles in cell adhesion  migration  and chemotaxis as a mechanism for recruitment of leukocytes into the heart. This work elucidates the mutual spatiotemporal relationships between different epicardial subpopulations and assigns unique function to each during cardiac development. Understanding which mechanisms cells employ to establish a functional epicardium and to communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. Overall design: Single cell RNA sequencing of FACS purified larval cardiac zebrafish cells", null, "pubmed:32084358", null, "058 1 F04 KOsema3fb tbx18 1 reseq", "GSM3719027", null, "tissue:Heart|transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "058 1 F04 KOsema3fb tbx18 1 reseq", "Alignment to GRCz10 91 with STAR v2.4.2a outSJfilterCountUniqueMin  1  1  1  1   outSJfilterCountTotalMin 30 10 10 10   outSAMstrandField intronMotif   outFilterIntronMotifs RemoveNoncanonical BAM files with samtools v1.3 view  bS Sorting of BAM files with samtools v1.3 sort Removal of PCR duplicates from BAM files with samtools v1.3 rmdup Read counting with featureCounts v1.4.5 p1  p  B  a  t exon  g gene id Genome build: GRCz10 91 Supplementary files format and content: Tab delimited text files of raw counts on gene level Supplementary files format and content: featureCounts KOsema3fb.txt: Tab delimited text file raw counts before QC  Column 1 = Ensembl gene ID  column 2 = gene length in basepairs  column 3 = gene name  columns 4 151 = counts for each cell  colnames = gene id  gene length  gene name  cell names 1 151 Supplementary files format and content: featureCounts KOsema3fb reseq.txt: Tab delimited text file of resequenced samples raw counts before QC", "Heart", null, "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", null, "transgenic reporter:tbx18:myr Citrine|cell fluorescence:myr Citrine|age:5 dpf", "GSM3719027", "GSM3719027: 058 1 F04 KOsema3fb tbx18 1 reseq; Danio rerio; RNA Seq", "GSM3719027", null, "1", "Larvae were physically disrupted  hearts collected and dissociated using Trypsin/collagenase. Single cells were purified via FACS. Smartseq2  Illumina Nextera XT", "GEO Accession:GSM3719027", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP166782", null, null, "058-1-F04-KOsema3fb-tbx18-1_reseq_all_lanes_R1.fastq.gz", "fastq", 1132466748.0, 15352198.0, "GSM3719027 r1", "0:73.77 1:0", "A:287483650;C:275728373;G:284236125;T:284105636;N:912964", 73, 0, null, null, 287483650, 275728373, 284236125, 284105636, 912964, "SRX5669628", "SRS4612497", "SRA798477", "GEO", "University of Oxford", 1, 0.85479, null, 0.29074, null, 0.94787, null, 0.64434, null, 72, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2019-04-11", "Larval", "Larval", "Heart", "Cardiovascular System"]], "truncated": false, "filtered_table_rows_count": 803, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": [], "units": {}, "query": {"sql": "select rowid, [run.accession], [experiment.accession], [sample.accession], [study.accession], bioproject, [study.title], [study.alias], [study.type], [study.abstract], [study.attributes], [study.PMIDs], [sample.description], [sample.title], [sample.alias], [sample.centername], [sample.attributes], [GEOsample.title], [GEOsample.dataprocessing], [GEOsample.source], [GEOsample.treatmentprotocol], [GEOsample.extractprotocol], [GEOsample.growthprotocol], [GEOsample.characteristics], [GEOsample.accession], [experiment.title], [experiment.alias], [experiment.library_name], [experiment.design_description], [experiment.library_construction_protocol], [experiment.attributes], [experiment.library_strategy], [experiment.library_source], [experiment.library_selection], [experiment.library_layout], [experiment.platform], [experiment.instrument_model], [experiment.spot_descriptor], [experiment.study_ref], [run.title], [run.attributes], [run.filename], [run.semantic_name], [run.total_bases], [run.total_spots], [run.alias], [run.read_lengths], [run.base_counts], [run.r1_length], [run.r2_length], [run.r3_length], [run.r4_length], [run.Acount], [run.Ccount], [run.Gcount], [run.Tcount], [run.Ncount], [run.experiment], [run.pool_member], [submission.accession], [submission.srasource], [submission.bioprojectsource], [seqdetective.n_mates], [seqdetective.mapping_rate.mate1], [seqdetective.mapping_rate.mate2], [seqdetective.nofeature_rate.mate1], [seqdetective.nofeature_rate.mate2], [seqdetective.sparsity.mate1], [seqdetective.sparsity.mate2], [seqdetective.pos_strand_rate.mate1], [seqdetective.pos_strand_rate.mate2], [seqdetective.readlen.mate1], [seqdetective.readlen.mate2], [seqdetective.judgement.mate1], [seqdetective.judgement.mate2], [seqdetective.judgement.reason], platform_family, instrument_generation, read_bias, selection_class, prep_kit, sc_or_bulk, tech_class, technology, tech_variant, [submission.bioprojectsource.country], earliest_date, devstage_curation, devstage_curation_coarse, tissue_curation, tissue_curation_coarse from run_metadata where \"devstage_curation\" = :p0 and \"tissue_curation\" = :p1 order by rowid limit 101", "params": {"p0": "Larval", "p1": "Heart"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Larval&tissue_curation=Heart", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 803, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Larval&tissue_curation=Heart&experiment.library_strategy=RNA-Seq", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Larval&tissue_curation=Heart", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 786, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Larval&tissue_curation=Heart&experiment.library_source=TRANSCRIPTOMIC", "selected": false}, {"value": "TRANSCRIPTOMIC SINGLE CELL", "label": "TRANSCRIPTOMIC SINGLE CELL", "count": 17, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Larval&tissue_curation=Heart&experiment.library_source=TRANSCRIPTOMIC+SINGLE+CELL", "selected": false}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Larval&tissue_curation=Heart", "results": [{"value": "cDNA", "label": "cDNA", "count": 775, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Larval&tissue_curation=Heart&experiment.library_selection=cDNA", "selected": false}, {"value": "Oligo-dT", "label": "Oligo-dT", "count": 10, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Larval&tissue_curation=Heart&experiment.library_selection=Oligo-dT", "selected": false}, {"value": "PCR", "label": "PCR", "count": 8, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Larval&tissue_curation=Heart&experiment.library_selection=PCR", "selected": false}, {"value": "PolyA", "label": "PolyA", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Larval&tissue_curation=Heart&experiment.library_selection=PolyA", "selected": false}, {"value": "RT-PCR", "label": "RT-PCR", "count": 4, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Larval&tissue_curation=Heart&experiment.library_selection=RT-PCR", "selected": false}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Larval&tissue_curation=Heart", "results": [{"value": "PAIRED", "label": "PAIRED", "count": 710, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Larval&tissue_curation=Heart&experiment.library_layout=PAIRED", "selected": false}, {"value": "SINGLE", "label": "SINGLE", "count": 93, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Larval&tissue_curation=Heart&experiment.library_layout=SINGLE", "selected": false}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Larval&tissue_curation=Heart", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 789, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Larval&tissue_curation=Heart&experiment.platform=ILLUMINA", "selected": false}, {"value": "BGISEQ", "label": "BGISEQ", "count": 8, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Larval&tissue_curation=Heart&experiment.platform=BGISEQ", "selected": false}, {"value": "DNBSEQ", "label": "DNBSEQ", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Larval&tissue_curation=Heart&experiment.platform=DNBSEQ", "selected": false}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Larval&tissue_curation=Heart", "results": [{"value": "Larval", "label": "Larval", "count": 803, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Larval&tissue_curation=Heart&devstage_curation_coarse=Larval", "selected": false}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Larval&tissue_curation=Heart", "results": [{"value": "Larval", "label": "Larval", "count": 803, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?tissue_curation=Heart", "selected": true}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Larval&tissue_curation=Heart", "results": [{"value": "Cardiovascular System", "label": "Cardiovascular System", "count": 803, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Larval&tissue_curation=Heart&tissue_curation_coarse=Cardiovascular+System", "selected": false}], "truncated": false}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Larval&tissue_curation=Heart", "results": [{"value": "Heart", "label": "Heart", "count": 803, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Larval", "selected": true}], "truncated": false}, "technology": {"name": "technology", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Larval&tissue_curation=Heart", "results": [{"value": "smartseq", "label": "smartseq", "count": 687, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Larval&tissue_curation=Heart&technology=smartseq", "selected": false}, {"value": "unknown", "label": "unknown", "count": 68, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Larval&tissue_curation=Heart&technology=unknown", "selected": false}, {"value": "celseq", "label": "celseq", "count": 19, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Larval&tissue_curation=Heart&technology=celseq", "selected": false}, {"value": "10x", "label": "10x", "count": 17, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Larval&tissue_curation=Heart&technology=10x", "selected": false}, {"value": "bulk", "label": "bulk", "count": 12, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Larval&tissue_curation=Heart&technology=bulk", "selected": false}], "truncated": false}}, "suggested_facets": [], "next": "49880", "next_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Larval&tissue_curation=Heart&_next=49880", "private": false, "allow_execute_sql": true, "query_ms": 162.59454499231651}