{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"SINGLE\", tissue_curation = \"Lymphatic System\" and tissue_curation_coarse = \"Cardiovascular System\"", "rows": [[61414, "SRR12712225", "SRX9191123", "SRS7427095", "SRP285378", "PRJNA665656", "The RNA helicase Ddx21 controls Vegfc driven developmental lymphangiogenesis by balancing endothelial cell ribosome biogenesis and p53 p21 signalling [zebrafish]", "GSE158566", "Transcriptome Analysis", "The development of a differentiated and functional vasculature requires coordinated control of cell fate specification  lineage differentiation and vascular network growth. Cellular proliferation is spatiotemporally regulated in developing vessel networks but how this is achieved and differentially controlled in specific lineages is unknown. Using a zebrafish forward genetic screen for mutants that form blood vessels but fail to form lymphatic vessels  we uncovered a mutant for the RNA helicase Ddx21. Ddx21 cell autonomously regulates the early development of lymphatic endothelial cells. Ddx21 is essential for Vegfc Vegfr3 driven endothelial cell proliferation. Ddx21 is an established regulator of ribosomal RNA transcription and in the absence of Ddx21  mutant lymphatic endothelial cells show reduced ribosome biogenesis. Ultimately  loss of Ddx21 leads to a p53 p21 dependent cell cycle arrest that blocks embryonic lymphangiogenesis. Thus  the RNA helicase Ddx21 coordinates the endothelial cell proliferative response to Vegfc Vegfr3 signalling by balancing ribosome biogenesis and p53 p21 signalling. This mechanism may have therapeutic potential in diseases of excessive lymphangiogenesis such as in cancer metastasis or lymphatic malformation. Overall design: LEC and VEC RNA profiles on sibling and ddx21 mutant cells obtained from zebrafish embryos", "parent bioproject:PRJNA748172", null, null, "ddx21 sibling 02", "GSM4802983", null, "tissue:ddx21 sibling|genotype/variation:ddx21 sibling|abbreviatedname:Sib 02|cell type:venous and lymphatic ECs VECs  LECs", "ddx21 sibling 02", "Sequenced reads were assessed for quality using fastqc and aligned and summarized using Subread V2.0.0 functions align and featureCount with default settings Filtering and normalisation of tag counts performed in edgeR using sequential functions filterByExpr  calcNormFactors and cpm A batch effect was removed in edgeR using removeBatchEffect function For plotting and differential expression analysis an offset of +1.0 and log2 transformation was applied Genome build: GRCz11 GCA 000002035.4 Supplementary files format and content: Matrix table with normalised  batch corredted and log2 transformed CPM for every gene and every sample", "ddx21 sibling", null, "At 3 dpf double positve cells were sorted from Tgfli1a:nEGFP;Tg5.2lyve1b:DsRed to isolate LECs and VECs RNA libraries were prepared for sequencing using standard Illumina protocols", null, "genotype/variation:ddx21 sibling|abbreviatedname:Sib 02|cell type:venous and lymphatic ECs VECs  LECs", "GSM4802983", "GSM4802983: ddx21 sibling 02; Danio rerio; RNA Seq", "GSM4802983", null, "1", "At 3 dpf double positve cells were sorted from Tgfli1a:nEGFP;Tg5.2lyve1b:DsRed to isolate LECs and VECs RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM4802983", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP285378", null, null, "4-DDX_sibling2_S5_R1_001.fastq", "fastq", 4132086148.0, 54841271.0, "GSM4802983 r1", "0:75.35 1:0", "A:1143149123;C:915565985;G:945819940;T:1127493713;N:57387", 75, 0, null, null, 1143149123, 915565985, 945819940, 1127493713, 57387, "SRX9191123", "SRS7427095", "SRA1131557", "GEO", "Hogan Laboratory, Program in Organogenesis and Cancer, Peter MacCallum Cancer Centre", 1, 0.93153, null, 0.15182, null, 0.73127, null, 0.47996, null, 75, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2020-09-25", "Larval", "Larval", "Lymphatic System", "Cardiovascular System"], [61415, "SRR12712224", "SRX9191122", "SRS7427094", "SRP285378", "PRJNA665656", "The RNA helicase Ddx21 controls Vegfc driven developmental lymphangiogenesis by balancing endothelial cell ribosome biogenesis and p53 p21 signalling [zebrafish]", "GSE158566", "Transcriptome Analysis", "The development of a differentiated and functional vasculature requires coordinated control of cell fate specification  lineage differentiation and vascular network growth. Cellular proliferation is spatiotemporally regulated in developing vessel networks but how this is achieved and differentially controlled in specific lineages is unknown. Using a zebrafish forward genetic screen for mutants that form blood vessels but fail to form lymphatic vessels  we uncovered a mutant for the RNA helicase Ddx21. Ddx21 cell autonomously regulates the early development of lymphatic endothelial cells. Ddx21 is essential for Vegfc Vegfr3 driven endothelial cell proliferation. Ddx21 is an established regulator of ribosomal RNA transcription and in the absence of Ddx21  mutant lymphatic endothelial cells show reduced ribosome biogenesis. Ultimately  loss of Ddx21 leads to a p53 p21 dependent cell cycle arrest that blocks embryonic lymphangiogenesis. Thus  the RNA helicase Ddx21 coordinates the endothelial cell proliferative response to Vegfc Vegfr3 signalling by balancing ribosome biogenesis and p53 p21 signalling. This mechanism may have therapeutic potential in diseases of excessive lymphangiogenesis such as in cancer metastasis or lymphatic malformation. Overall design: LEC and VEC RNA profiles on sibling and ddx21 mutant cells obtained from zebrafish embryos", "parent bioproject:PRJNA748172", null, null, "ddx21 mutant 02", "GSM4802982", null, "tissue:ddx21 mutant|genotype/variation:ddx21 mutant|abbreviatedname:Mut 02|cell type:venous and lymphatic ECs VECs  LECs", "ddx21 mutant 02", "Sequenced reads were assessed for quality using fastqc and aligned and summarized using Subread V2.0.0 functions align and featureCount with default settings Filtering and normalisation of tag counts performed in edgeR using sequential functions filterByExpr  calcNormFactors and cpm A batch effect was removed in edgeR using removeBatchEffect function For plotting and differential expression analysis an offset of +1.0 and log2 transformation was applied Genome build: GRCz11 GCA 000002035.4 Supplementary files format and content: Matrix table with normalised  batch corredted and log2 transformed CPM for every gene and every sample", "ddx21 mutant", null, "At 3 dpf double positve cells were sorted from Tgfli1a:nEGFP;Tg5.2lyve1b:DsRed to isolate LECs and VECs RNA libraries were prepared for sequencing using standard Illumina protocols", null, "genotype/variation:ddx21 mutant|abbreviatedname:Mut 02|cell type:venous and lymphatic ECs VECs  LECs", "GSM4802982", "GSM4802982: ddx21 mutant 02; Danio rerio; RNA Seq", "GSM4802982", null, "1", "At 3 dpf double positve cells were sorted from Tgfli1a:nEGFP;Tg5.2lyve1b:DsRed to isolate LECs and VECs RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM4802982", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP285378", null, null, "3-DDX1_mutant2_S6_R1_001.fastq", "fastq", 4489565415.0, 59577710.0, "GSM4802982 r1", "0:75.36 1:0", "A:1250571429;C:986785347;G:1019382421;T:1232761308;N:64910", 75, 0, null, null, 1250571429, 986785347, 1019382421, 1232761308, 64910, "SRX9191122", "SRS7427094", "SRA1131557", "GEO", "Hogan Laboratory, Program in Organogenesis and Cancer, Peter MacCallum Cancer Centre", 1, 0.93491, null, 0.11271, null, 0.7399, null, 0.48877, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2020-09-25", "Larval", "Larval", "Lymphatic System", "Cardiovascular System"], [61416, "SRR12712223", "SRX9191121", "SRS7427093", "SRP285378", "PRJNA665656", "The RNA helicase Ddx21 controls Vegfc driven developmental lymphangiogenesis by balancing endothelial cell ribosome biogenesis and p53 p21 signalling [zebrafish]", "GSE158566", "Transcriptome Analysis", "The development of a differentiated and functional vasculature requires coordinated control of cell fate specification  lineage differentiation and vascular network growth. Cellular proliferation is spatiotemporally regulated in developing vessel networks but how this is achieved and differentially controlled in specific lineages is unknown. Using a zebrafish forward genetic screen for mutants that form blood vessels but fail to form lymphatic vessels  we uncovered a mutant for the RNA helicase Ddx21. Ddx21 cell autonomously regulates the early development of lymphatic endothelial cells. Ddx21 is essential for Vegfc Vegfr3 driven endothelial cell proliferation. Ddx21 is an established regulator of ribosomal RNA transcription and in the absence of Ddx21  mutant lymphatic endothelial cells show reduced ribosome biogenesis. Ultimately  loss of Ddx21 leads to a p53 p21 dependent cell cycle arrest that blocks embryonic lymphangiogenesis. Thus  the RNA helicase Ddx21 coordinates the endothelial cell proliferative response to Vegfc Vegfr3 signalling by balancing ribosome biogenesis and p53 p21 signalling. This mechanism may have therapeutic potential in diseases of excessive lymphangiogenesis such as in cancer metastasis or lymphatic malformation. Overall design: LEC and VEC RNA profiles on sibling and ddx21 mutant cells obtained from zebrafish embryos", "parent bioproject:PRJNA748172", null, null, "ddx21 sibling 01", "GSM4802981", null, "tissue:ddx21 sibling|genotype/variation:ddx21 sibling|abbreviatedname:Sib 01|cell type:venous and lymphatic ECs VECs  LECs", "ddx21 sibling 01", "Sequenced reads were assessed for quality using fastqc and aligned and summarized using Subread V2.0.0 functions align and featureCount with default settings Filtering and normalisation of tag counts performed in edgeR using sequential functions filterByExpr  calcNormFactors and cpm A batch effect was removed in edgeR using removeBatchEffect function For plotting and differential expression analysis an offset of +1.0 and log2 transformation was applied Genome build: GRCz11 GCA 000002035.4 Supplementary files format and content: Matrix table with normalised  batch corredted and log2 transformed CPM for every gene and every sample", "ddx21 sibling", null, "At 3 dpf double positve cells were sorted from Tgfli1a:nEGFP;Tg5.2lyve1b:DsRed to isolate LECs and VECs RNA libraries were prepared for sequencing using standard Illumina protocols", null, "genotype/variation:ddx21 sibling|abbreviatedname:Sib 01|cell type:venous and lymphatic ECs VECs  LECs", "GSM4802981", "GSM4802981: ddx21 sibling 01; Danio rerio; RNA Seq", "GSM4802981", null, "1", "At 3 dpf double positve cells were sorted from Tgfli1a:nEGFP;Tg5.2lyve1b:DsRed to isolate LECs and VECs RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM4802981", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP285378", null, null, "2-DDX_sibling1_S7_R1_001.fastq", "fastq", 3962887115.0, 52588574.0, "GSM4802981 r1", "0:75.36 1:0", "A:1113967875;C:858353708;G:888913973;T:1101593170;N:58389", 75, 0, null, null, 1113967875, 858353708, 888913973, 1101593170, 58389, "SRX9191121", "SRS7427093", "SRA1131557", "GEO", "Hogan Laboratory, Program in Organogenesis and Cancer, Peter MacCallum Cancer Centre", 1, 0.92594, null, 0.17769, null, 0.72143, null, 0.49105, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2020-09-25", "Larval", "Larval", "Lymphatic System", "Cardiovascular System"], [61417, "SRR12712222", "SRX9191120", "SRS7427092", "SRP285378", "PRJNA665656", "The RNA helicase Ddx21 controls Vegfc driven developmental lymphangiogenesis by balancing endothelial cell ribosome biogenesis and p53 p21 signalling [zebrafish]", "GSE158566", "Transcriptome Analysis", "The development of a differentiated and functional vasculature requires coordinated control of cell fate specification  lineage differentiation and vascular network growth. Cellular proliferation is spatiotemporally regulated in developing vessel networks but how this is achieved and differentially controlled in specific lineages is unknown. Using a zebrafish forward genetic screen for mutants that form blood vessels but fail to form lymphatic vessels  we uncovered a mutant for the RNA helicase Ddx21. Ddx21 cell autonomously regulates the early development of lymphatic endothelial cells. Ddx21 is essential for Vegfc Vegfr3 driven endothelial cell proliferation. Ddx21 is an established regulator of ribosomal RNA transcription and in the absence of Ddx21  mutant lymphatic endothelial cells show reduced ribosome biogenesis. Ultimately  loss of Ddx21 leads to a p53 p21 dependent cell cycle arrest that blocks embryonic lymphangiogenesis. Thus  the RNA helicase Ddx21 coordinates the endothelial cell proliferative response to Vegfc Vegfr3 signalling by balancing ribosome biogenesis and p53 p21 signalling. This mechanism may have therapeutic potential in diseases of excessive lymphangiogenesis such as in cancer metastasis or lymphatic malformation. Overall design: LEC and VEC RNA profiles on sibling and ddx21 mutant cells obtained from zebrafish embryos", "parent bioproject:PRJNA748172", null, null, "ddx21 mutant 01", "GSM4802980", null, "tissue:ddx21 mutant|genotype/variation:ddx21 mutant|abbreviatedname:Mut 01|cell type:venous and lymphatic ECs VECs  LECs", "ddx21 mutant 01", "Sequenced reads were assessed for quality using fastqc and aligned and summarized using Subread V2.0.0 functions align and featureCount with default settings Filtering and normalisation of tag counts performed in edgeR using sequential functions filterByExpr  calcNormFactors and cpm A batch effect was removed in edgeR using removeBatchEffect function For plotting and differential expression analysis an offset of +1.0 and log2 transformation was applied Genome build: GRCz11 GCA 000002035.4 Supplementary files format and content: Matrix table with normalised  batch corredted and log2 transformed CPM for every gene and every sample", "ddx21 mutant", null, "At 3 dpf double positve cells were sorted from Tgfli1a:nEGFP;Tg5.2lyve1b:DsRed to isolate LECs and VECs RNA libraries were prepared for sequencing using standard Illumina protocols", null, "genotype/variation:ddx21 mutant|abbreviatedname:Mut 01|cell type:venous and lymphatic ECs VECs  LECs", "GSM4802980", "GSM4802980: ddx21 mutant 01; Danio rerio; RNA Seq", "GSM4802980", null, "1", "At 3 dpf double positve cells were sorted from Tgfli1a:nEGFP;Tg5.2lyve1b:DsRed to isolate LECs and VECs RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM4802980", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP285378", null, null, "1-DDX1_mutant1_S8_R1_001.fastq", "fastq", 4172788466.0, 55358419.0, "GSM4802980 r1", "0:75.38 1:0", "A:1157297483;C:922321451;G:952921150;T:1140193401;N:54981", 75, 0, null, null, 1157297483, 922321451, 952921150, 1140193401, 54981, "SRX9191120", "SRS7427092", "SRA1131557", "GEO", "Hogan Laboratory, Program in Organogenesis and Cancer, Peter MacCallum Cancer Centre", 1, 0.93753, null, 0.11708, null, 0.75022, null, 0.4679, null, 74, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2020-09-25", "Larval", "Larval", "Lymphatic System", "Cardiovascular System"], [61418, "SRR12712229", "SRX9191119", "SRS7427091", "SRP285378", "PRJNA665656", "The RNA helicase Ddx21 controls Vegfc driven developmental lymphangiogenesis by balancing endothelial cell ribosome biogenesis and p53 p21 signalling [zebrafish]", "GSE158566", "Transcriptome Analysis", "The development of a differentiated and functional vasculature requires coordinated control of cell fate specification  lineage differentiation and vascular network growth. Cellular proliferation is spatiotemporally regulated in developing vessel networks but how this is achieved and differentially controlled in specific lineages is unknown. Using a zebrafish forward genetic screen for mutants that form blood vessels but fail to form lymphatic vessels  we uncovered a mutant for the RNA helicase Ddx21. Ddx21 cell autonomously regulates the early development of lymphatic endothelial cells. Ddx21 is essential for Vegfc Vegfr3 driven endothelial cell proliferation. Ddx21 is an established regulator of ribosomal RNA transcription and in the absence of Ddx21  mutant lymphatic endothelial cells show reduced ribosome biogenesis. Ultimately  loss of Ddx21 leads to a p53 p21 dependent cell cycle arrest that blocks embryonic lymphangiogenesis. Thus  the RNA helicase Ddx21 coordinates the endothelial cell proliferative response to Vegfc Vegfr3 signalling by balancing ribosome biogenesis and p53 p21 signalling. This mechanism may have therapeutic potential in diseases of excessive lymphangiogenesis such as in cancer metastasis or lymphatic malformation. Overall design: LEC and VEC RNA profiles on sibling and ddx21 mutant cells obtained from zebrafish embryos", "parent bioproject:PRJNA748172", null, null, "ddx21 sibling 04", "GSM4802987", null, "tissue:ddx21 sibling|genotype/variation:ddx21 sibling|abbreviatedname:Sib 04|cell type:venous and lymphatic ECs VECs  LECs", "ddx21 sibling 04", "Sequenced reads were assessed for quality using fastqc and aligned and summarized using Subread V2.0.0 functions align and featureCount with default settings Filtering and normalisation of tag counts performed in edgeR using sequential functions filterByExpr  calcNormFactors and cpm A batch effect was removed in edgeR using removeBatchEffect function For plotting and differential expression analysis an offset of +1.0 and log2 transformation was applied Genome build: GRCz11 GCA 000002035.4 Supplementary files format and content: Matrix table with normalised  batch corredted and log2 transformed CPM for every gene and every sample", "ddx21 sibling", null, "At 3 dpf double positve cells were sorted from Tgfli1a:nEGFP;Tg5.2lyve1b:DsRed to isolate LECs and VECs RNA libraries were prepared for sequencing using standard Illumina protocols", null, "genotype/variation:ddx21 sibling|abbreviatedname:Sib 04|cell type:venous and lymphatic ECs VECs  LECs", "GSM4802987", "GSM4802987: ddx21 sibling 04; Danio rerio; RNA Seq", "GSM4802987", null, "1", "At 3 dpf double positve cells were sorted from Tgfli1a:nEGFP;Tg5.2lyve1b:DsRed to isolate LECs and VECs RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM4802987", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP285378", null, null, "8-DDX_sibling4_S1_R1_001.fastq", "fastq", 4915017825.0, 65191268.0, "GSM4802987 r1", "0:75.39 1:0", "A:1371356175;C:1074769694;G:1111138012;T:1357694052;N:59892", 75, 0, null, null, 1371356175, 1074769694, 1111138012, 1357694052, 59892, "SRX9191119", "SRS7427091", "SRA1131557", "GEO", "Hogan Laboratory, Program in Organogenesis and Cancer, Peter MacCallum Cancer Centre", 1, 0.93029, null, 0.13059, null, 0.76288, null, 0.49579, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2020-09-25", "Larval", "Larval", "Lymphatic System", "Cardiovascular System"], [61419, "SRR12712228", "SRX9191118", "SRS7427090", "SRP285378", "PRJNA665656", "The RNA helicase Ddx21 controls Vegfc driven developmental lymphangiogenesis by balancing endothelial cell ribosome biogenesis and p53 p21 signalling [zebrafish]", "GSE158566", "Transcriptome Analysis", "The development of a differentiated and functional vasculature requires coordinated control of cell fate specification  lineage differentiation and vascular network growth. Cellular proliferation is spatiotemporally regulated in developing vessel networks but how this is achieved and differentially controlled in specific lineages is unknown. Using a zebrafish forward genetic screen for mutants that form blood vessels but fail to form lymphatic vessels  we uncovered a mutant for the RNA helicase Ddx21. Ddx21 cell autonomously regulates the early development of lymphatic endothelial cells. Ddx21 is essential for Vegfc Vegfr3 driven endothelial cell proliferation. Ddx21 is an established regulator of ribosomal RNA transcription and in the absence of Ddx21  mutant lymphatic endothelial cells show reduced ribosome biogenesis. Ultimately  loss of Ddx21 leads to a p53 p21 dependent cell cycle arrest that blocks embryonic lymphangiogenesis. Thus  the RNA helicase Ddx21 coordinates the endothelial cell proliferative response to Vegfc Vegfr3 signalling by balancing ribosome biogenesis and p53 p21 signalling. This mechanism may have therapeutic potential in diseases of excessive lymphangiogenesis such as in cancer metastasis or lymphatic malformation. Overall design: LEC and VEC RNA profiles on sibling and ddx21 mutant cells obtained from zebrafish embryos", "parent bioproject:PRJNA748172", null, null, "ddx21 mutant 04", "GSM4802986", null, "tissue:ddx21 mutant|genotype/variation:ddx21 mutant|abbreviatedname:Mut 04|cell type:venous and lymphatic ECs VECs  LECs", "ddx21 mutant 04", "Sequenced reads were assessed for quality using fastqc and aligned and summarized using Subread V2.0.0 functions align and featureCount with default settings Filtering and normalisation of tag counts performed in edgeR using sequential functions filterByExpr  calcNormFactors and cpm A batch effect was removed in edgeR using removeBatchEffect function For plotting and differential expression analysis an offset of +1.0 and log2 transformation was applied Genome build: GRCz11 GCA 000002035.4 Supplementary files format and content: Matrix table with normalised  batch corredted and log2 transformed CPM for every gene and every sample", "ddx21 mutant", null, "At 3 dpf double positve cells were sorted from Tgfli1a:nEGFP;Tg5.2lyve1b:DsRed to isolate LECs and VECs RNA libraries were prepared for sequencing using standard Illumina protocols", null, "genotype/variation:ddx21 mutant|abbreviatedname:Mut 04|cell type:venous and lymphatic ECs VECs  LECs", "GSM4802986", "GSM4802986: ddx21 mutant 04; Danio rerio; RNA Seq", "GSM4802986", null, "1", "At 3 dpf double positve cells were sorted from Tgfli1a:nEGFP;Tg5.2lyve1b:DsRed to isolate LECs and VECs RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM4802986", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP285378", null, null, "7-DDX1_mutant4_S2_R1_001.fastq", "fastq", 4934798895.0, 65454382.0, "GSM4802986 r1", "0:75.39 1:0", "A:1386796418;C:1074595432;G:1108772428;T:1364575960;N:58657", 75, 0, null, null, 1386796418, 1074595432, 1108772428, 1364575960, 58657, "SRX9191118", "SRS7427090", "SRA1131557", "GEO", "Hogan Laboratory, Program in Organogenesis and Cancer, Peter MacCallum Cancer Centre", 1, 0.93352, null, 0.1274, null, 0.75276, null, 0.49744, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2020-09-25", "Larval", "Larval", "Lymphatic System", "Cardiovascular System"], [61420, "SRR12712227", "SRX9191117", "SRS7427089", "SRP285378", "PRJNA665656", "The RNA helicase Ddx21 controls Vegfc driven developmental lymphangiogenesis by balancing endothelial cell ribosome biogenesis and p53 p21 signalling [zebrafish]", "GSE158566", "Transcriptome Analysis", "The development of a differentiated and functional vasculature requires coordinated control of cell fate specification  lineage differentiation and vascular network growth. Cellular proliferation is spatiotemporally regulated in developing vessel networks but how this is achieved and differentially controlled in specific lineages is unknown. Using a zebrafish forward genetic screen for mutants that form blood vessels but fail to form lymphatic vessels  we uncovered a mutant for the RNA helicase Ddx21. Ddx21 cell autonomously regulates the early development of lymphatic endothelial cells. Ddx21 is essential for Vegfc Vegfr3 driven endothelial cell proliferation. Ddx21 is an established regulator of ribosomal RNA transcription and in the absence of Ddx21  mutant lymphatic endothelial cells show reduced ribosome biogenesis. Ultimately  loss of Ddx21 leads to a p53 p21 dependent cell cycle arrest that blocks embryonic lymphangiogenesis. Thus  the RNA helicase Ddx21 coordinates the endothelial cell proliferative response to Vegfc Vegfr3 signalling by balancing ribosome biogenesis and p53 p21 signalling. This mechanism may have therapeutic potential in diseases of excessive lymphangiogenesis such as in cancer metastasis or lymphatic malformation. Overall design: LEC and VEC RNA profiles on sibling and ddx21 mutant cells obtained from zebrafish embryos", "parent bioproject:PRJNA748172", null, null, "ddx21 sibling 03", "GSM4802985", null, "tissue:ddx21 sibling|genotype/variation:ddx21 sibling|abbreviatedname:Sib 03|cell type:venous and lymphatic ECs VECs  LECs", "ddx21 sibling 03", "Sequenced reads were assessed for quality using fastqc and aligned and summarized using Subread V2.0.0 functions align and featureCount with default settings Filtering and normalisation of tag counts performed in edgeR using sequential functions filterByExpr  calcNormFactors and cpm A batch effect was removed in edgeR using removeBatchEffect function For plotting and differential expression analysis an offset of +1.0 and log2 transformation was applied Genome build: GRCz11 GCA 000002035.4 Supplementary files format and content: Matrix table with normalised  batch corredted and log2 transformed CPM for every gene and every sample", "ddx21 sibling", null, "At 3 dpf double positve cells were sorted from Tgfli1a:nEGFP;Tg5.2lyve1b:DsRed to isolate LECs and VECs RNA libraries were prepared for sequencing using standard Illumina protocols", null, "genotype/variation:ddx21 sibling|abbreviatedname:Sib 03|cell type:venous and lymphatic ECs VECs  LECs", "GSM4802985", "GSM4802985: ddx21 sibling 03; Danio rerio; RNA Seq", "GSM4802985", null, "1", "At 3 dpf double positve cells were sorted from Tgfli1a:nEGFP;Tg5.2lyve1b:DsRed to isolate LECs and VECs RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM4802985", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP285378", null, null, "6-DDX_sibling3_S3_R1_001.fastq", "fastq", 4686029757.0, 62155887.0, "GSM4802985 r1", "0:75.39 1:0", "A:1310041056;C:1025050637;G:1061770975;T:1289110659;N:56430", 75, 0, null, null, 1310041056, 1025050637, 1061770975, 1289110659, 56430, "SRX9191117", "SRS7427089", "SRA1131557", "GEO", "Hogan Laboratory, Program in Organogenesis and Cancer, Peter MacCallum Cancer Centre", 1, 0.93421, null, 0.13013, null, 0.74468, null, 0.50075, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2020-09-25", "Larval", "Larval", "Lymphatic System", "Cardiovascular System"], [61421, "SRR12712226", "SRX9191116", "SRS7427088", "SRP285378", "PRJNA665656", "The RNA helicase Ddx21 controls Vegfc driven developmental lymphangiogenesis by balancing endothelial cell ribosome biogenesis and p53 p21 signalling [zebrafish]", "GSE158566", "Transcriptome Analysis", "The development of a differentiated and functional vasculature requires coordinated control of cell fate specification  lineage differentiation and vascular network growth. Cellular proliferation is spatiotemporally regulated in developing vessel networks but how this is achieved and differentially controlled in specific lineages is unknown. Using a zebrafish forward genetic screen for mutants that form blood vessels but fail to form lymphatic vessels  we uncovered a mutant for the RNA helicase Ddx21. Ddx21 cell autonomously regulates the early development of lymphatic endothelial cells. Ddx21 is essential for Vegfc Vegfr3 driven endothelial cell proliferation. Ddx21 is an established regulator of ribosomal RNA transcription and in the absence of Ddx21  mutant lymphatic endothelial cells show reduced ribosome biogenesis. Ultimately  loss of Ddx21 leads to a p53 p21 dependent cell cycle arrest that blocks embryonic lymphangiogenesis. Thus  the RNA helicase Ddx21 coordinates the endothelial cell proliferative response to Vegfc Vegfr3 signalling by balancing ribosome biogenesis and p53 p21 signalling. This mechanism may have therapeutic potential in diseases of excessive lymphangiogenesis such as in cancer metastasis or lymphatic malformation. Overall design: LEC and VEC RNA profiles on sibling and ddx21 mutant cells obtained from zebrafish embryos", "parent bioproject:PRJNA748172", null, null, "ddx21 mutant 03", "GSM4802984", null, "tissue:ddx21 mutant|genotype/variation:ddx21 mutant|abbreviatedname:Mut 03|cell type:venous and lymphatic ECs VECs  LECs", "ddx21 mutant 03", "Sequenced reads were assessed for quality using fastqc and aligned and summarized using Subread V2.0.0 functions align and featureCount with default settings Filtering and normalisation of tag counts performed in edgeR using sequential functions filterByExpr  calcNormFactors and cpm A batch effect was removed in edgeR using removeBatchEffect function For plotting and differential expression analysis an offset of +1.0 and log2 transformation was applied Genome build: GRCz11 GCA 000002035.4 Supplementary files format and content: Matrix table with normalised  batch corredted and log2 transformed CPM for every gene and every sample", "ddx21 mutant", null, "At 3 dpf double positve cells were sorted from Tgfli1a:nEGFP;Tg5.2lyve1b:DsRed to isolate LECs and VECs RNA libraries were prepared for sequencing using standard Illumina protocols", null, "genotype/variation:ddx21 mutant|abbreviatedname:Mut 03|cell type:venous and lymphatic ECs VECs  LECs", "GSM4802984", "GSM4802984: ddx21 mutant 03; Danio rerio; RNA Seq", "GSM4802984", null, "1", "At 3 dpf double positve cells were sorted from Tgfli1a:nEGFP;Tg5.2lyve1b:DsRed to isolate LECs and VECs RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM4802984", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP285378", null, null, "5-DDX1_mutant3_S4_R1_001.fastq", "fastq", 4774244717.0, 63335788.0, "GSM4802984 r1", "0:75.38 1:0", "A:1333800977;C:1045188899;G:1081436862;T:1313758360;N:59619", 75, 0, null, null, 1333800977, 1045188899, 1081436862, 1313758360, 59619, "SRX9191116", "SRS7427088", "SRA1131557", "GEO", "Hogan Laboratory, Program in Organogenesis and Cancer, Peter MacCallum Cancer Centre", 1, 0.93177, null, 0.13392, null, 0.73864, null, 0.49841, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2020-09-25", "Larval", "Larval", "Lymphatic System", "Cardiovascular System"]], "truncated": false, "filtered_table_rows_count": 8, "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 \"experiment.library_layout\" = :p0 and \"tissue_curation\" = :p1 and \"tissue_curation_coarse\" = :p2 order by rowid limit 101", "params": {"p0": "SINGLE", "p1": "Lymphatic System", "p2": "Cardiovascular System"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation=Lymphatic+System&tissue_curation_coarse=Cardiovascular+System", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 8, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation=Lymphatic+System&tissue_curation_coarse=Cardiovascular+System&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?experiment.library_layout=SINGLE&tissue_curation=Lymphatic+System&tissue_curation_coarse=Cardiovascular+System", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 8, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation=Lymphatic+System&tissue_curation_coarse=Cardiovascular+System&experiment.library_source=TRANSCRIPTOMIC", "selected": false}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation=Lymphatic+System&tissue_curation_coarse=Cardiovascular+System", "results": [{"value": "cDNA", "label": "cDNA", "count": 8, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation=Lymphatic+System&tissue_curation_coarse=Cardiovascular+System&experiment.library_selection=cDNA", "selected": false}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation=Lymphatic+System&tissue_curation_coarse=Cardiovascular+System", "results": [{"value": "SINGLE", "label": "SINGLE", "count": 8, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?tissue_curation=Lymphatic+System&tissue_curation_coarse=Cardiovascular+System", "selected": true}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation=Lymphatic+System&tissue_curation_coarse=Cardiovascular+System", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 8, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation=Lymphatic+System&tissue_curation_coarse=Cardiovascular+System&experiment.platform=ILLUMINA", "selected": false}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation=Lymphatic+System&tissue_curation_coarse=Cardiovascular+System", "results": [{"value": "Larval", "label": "Larval", "count": 8, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation=Lymphatic+System&tissue_curation_coarse=Cardiovascular+System&devstage_curation_coarse=Larval", "selected": false}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation=Lymphatic+System&tissue_curation_coarse=Cardiovascular+System", "results": [{"value": "Larval", "label": "Larval", "count": 8, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation=Lymphatic+System&tissue_curation_coarse=Cardiovascular+System&devstage_curation=Larval", "selected": false}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation=Lymphatic+System&tissue_curation_coarse=Cardiovascular+System", "results": [{"value": "Cardiovascular System", "label": "Cardiovascular System", "count": 8, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation=Lymphatic+System", "selected": true}], "truncated": false}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation=Lymphatic+System&tissue_curation_coarse=Cardiovascular+System", "results": [{"value": "Lymphatic System", "label": "Lymphatic System", "count": 8, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation_coarse=Cardiovascular+System", "selected": true}], "truncated": false}, "technology": {"name": "technology", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation=Lymphatic+System&tissue_curation_coarse=Cardiovascular+System", "results": [{"value": "unknown", "label": "unknown", "count": 8, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_layout=SINGLE&tissue_curation=Lymphatic+System&tissue_curation_coarse=Cardiovascular+System&technology=unknown", "selected": false}], "truncated": false}}, "suggested_facets": [], "next": null, "next_url": null, "private": false, "allow_execute_sql": true, "query_ms": 101.04035299991665}