{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Undetermined\" and tissue_curation = \"Endothelium\"", "rows": [[41681, "SRR5119926", "SRX2435201", "SRS1870197", "SRP095331", "PRJNA358009", "CXCL8 and CXCR1 Remodel the Vascular Niche to Promote Hematopoietic Stem and Progenitor Cell Colonization and Engraftment [wt vs kdrl:cxcr1]", "GSE92542", "Transcriptome Analysis", "The microenvironment is an important regulator of hematopoietic stem and progenitor cell HSPC biology.  Interactions between the niche and stem cells have been difficult to track  but recent advances marking fluorescent HSPCs have allowed exquisite visualization in the caudal hematopoietic tissue CHT of the developing zebrafish.  Sinusoidal endothelial cells interact closely with HSPCs as they colonize this niche.  Here we show that the chemokine cxcl8 and its receptor  cxcr1  are abundantly expressed by zebrafish endothelial cells and we identify cxcl8/cxcr1 signaling as a positive regulator of HSPC colonization using genetic gain  and loss of function techniques.  Single cell tracking experiments demonstrated that this effect is due to an increase in HSPC \u201ccuddling\u201d by endothelial cells  thereby increasing CHT residency time and allowing more HSPC cell divisions to occur.  Enhanced cxcl8/cxcr1 signaling was associated with an increase in the volume of the CHT and induction of cxcl12a expression  favoring HSPC colonization.  Finally  using parabiotic zebrafish  we show that cxcr1 acts stem cell non autonomously to improve the efficiency of donor HSPC engraftment.  This work identifies a mechanism by which the hematopoietic niche remodels to promote HSPC engraftment and suggests that cxcl8/cxcr1 signaling is a potential therapeutic target in patients undergoing hematopoietic stem cell transplantation. Overall design: Kdrl:mcherry and kdrl:mcherry;kdrl:cxcr1 zebrafish were dissociated and endothelial cells purified by FACS.  RNA seq libraries were prepared from endothelial cells purified from two independent clutches of fish four libraries total.", "parent bioproject:PRJNA358001", "pubmed:28351983", null, "wt clutch2", "GSM2432105", null, "tissue:endothelial cells|cell type:endothelial cells", "wt clutch2", "Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using cutadapt  then mapped to Ensembl GRCz10 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz10 Supplementary files format and content: excel files include RPKM values for each Sample", "endothelial cells", null, "Freshly sorted cells were lysed in Trizol LS and total RNA was extracted by isopropanol precipitation. Libraries were prepared using the SMARTer Universal Low Input RNA kit followed by the Low Input Library Prep Kit for Illumina Clontech Laboratories.", "Zebrafish embryos were grown under standard conditions in a 28 degree incubator.", "cell type:endothelial cells", "GSM2432105", "GSM2432105: wt clutch2; Danio rerio; RNA Seq", "GSM2432105", null, "1", "Freshly sorted cells were lysed in Trizol LS and total RNA was extracted by isopropanol precipitation. Libraries were prepared using the SMARTer Universal Low Input RNA kit followed by the Low Input Library Prep Kit for Illumina Clontech Laboratories.", "GEO Accession:GSM2432105", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP095331", null, null, "BB-IL8-7_GATCAG_R2.fastq.gz BB-IL8-7_GATCAG_R1.fastq.gz", "fastq fastq", 6054362200.0, 30271811.0, "GSM2432105 r1", "0:100 1:100", "A:1586036726;C:1442511502;G:1449390272;T:1575855416;N:568284", 100, 100, null, null, 1586036726, 1442511502, 1449390272, 1575855416, 568284, "SRX2435201", "SRS1870197", "SRA505250", "GEO", "Oncology/Hematology, Boston Children's Hospital", 2, 0.68659, 0.68507, 0.22283, 0.22137, 0.76067, 0.76343, 0.57225, 0.58743, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "random_priming", "smarter", "bulk", "unknown", "unknown", null, "United States", "2016-12-19", "Undetermined", "Embryo", "Endothelium", "Cardiovascular System"], [41682, "SRR5119925", "SRX2435200", "SRS1870195", "SRP095331", "PRJNA358009", "CXCL8 and CXCR1 Remodel the Vascular Niche to Promote Hematopoietic Stem and Progenitor Cell Colonization and Engraftment [wt vs kdrl:cxcr1]", "GSE92542", "Transcriptome Analysis", "The microenvironment is an important regulator of hematopoietic stem and progenitor cell HSPC biology.  Interactions between the niche and stem cells have been difficult to track  but recent advances marking fluorescent HSPCs have allowed exquisite visualization in the caudal hematopoietic tissue CHT of the developing zebrafish.  Sinusoidal endothelial cells interact closely with HSPCs as they colonize this niche.  Here we show that the chemokine cxcl8 and its receptor  cxcr1  are abundantly expressed by zebrafish endothelial cells and we identify cxcl8/cxcr1 signaling as a positive regulator of HSPC colonization using genetic gain  and loss of function techniques.  Single cell tracking experiments demonstrated that this effect is due to an increase in HSPC \u201ccuddling\u201d by endothelial cells  thereby increasing CHT residency time and allowing more HSPC cell divisions to occur.  Enhanced cxcl8/cxcr1 signaling was associated with an increase in the volume of the CHT and induction of cxcl12a expression  favoring HSPC colonization.  Finally  using parabiotic zebrafish  we show that cxcr1 acts stem cell non autonomously to improve the efficiency of donor HSPC engraftment.  This work identifies a mechanism by which the hematopoietic niche remodels to promote HSPC engraftment and suggests that cxcl8/cxcr1 signaling is a potential therapeutic target in patients undergoing hematopoietic stem cell transplantation. Overall design: Kdrl:mcherry and kdrl:mcherry;kdrl:cxcr1 zebrafish were dissociated and endothelial cells purified by FACS.  RNA seq libraries were prepared from endothelial cells purified from two independent clutches of fish four libraries total.", "parent bioproject:PRJNA358001", "pubmed:28351983", null, "wt clutch1", "GSM2432104", null, "tissue:endothelial cells|cell type:endothelial cells", "wt clutch1", "Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using cutadapt  then mapped to Ensembl GRCz10 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz10 Supplementary files format and content: excel files include RPKM values for each Sample", "endothelial cells", null, "Freshly sorted cells were lysed in Trizol LS and total RNA was extracted by isopropanol precipitation. 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Libraries were prepared using the SMARTer Universal Low Input RNA kit followed by the Low Input Library Prep Kit for Illumina Clontech Laboratories.", "GEO Accession:GSM2432104", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP095331", null, null, "BB-IL8-3_TGACCA_R1.fastq.gz BB-IL8-3_TGACCA_R2.fastq.gz", "fastq fastq", 4718160000.0, 23590800.0, "GSM2432104 r1", "0:100 1:100", "A:1285175152;C:1075055485;G:1078285328;T:1279202852;N:441183", 100, 100, null, null, 1285175152, 1075055485, 1078285328, 1279202852, 441183, "SRX2435200", "SRS1870195", "SRA505250", "GEO", "Oncology/Hematology, Boston Children's Hospital", 2, 0.79676, 0.7947, 0.26445, 0.26272, 0.71652, 0.71924, 0.55157, 0.55957, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "random_priming", "smarter", "bulk", "unknown", "unknown", null, "United States", "2016-12-19", "Undetermined", "Embryo", "Endothelium", "Cardiovascular System"], [41683, "SRR5119924", "SRX2435199", "SRS1870196", "SRP095331", "PRJNA358009", "CXCL8 and CXCR1 Remodel the Vascular Niche to Promote Hematopoietic Stem and Progenitor Cell Colonization and Engraftment [wt vs kdrl:cxcr1]", "GSE92542", "Transcriptome Analysis", "The microenvironment is an important regulator of hematopoietic stem and progenitor cell HSPC biology.  Interactions between the niche and stem cells have been difficult to track  but recent advances marking fluorescent HSPCs have allowed exquisite visualization in the caudal hematopoietic tissue CHT of the developing zebrafish.  Sinusoidal endothelial cells interact closely with HSPCs as they colonize this niche.  Here we show that the chemokine cxcl8 and its receptor  cxcr1  are abundantly expressed by zebrafish endothelial cells and we identify cxcl8/cxcr1 signaling as a positive regulator of HSPC colonization using genetic gain  and loss of function techniques.  Single cell tracking experiments demonstrated that this effect is due to an increase in HSPC \u201ccuddling\u201d by endothelial cells  thereby increasing CHT residency time and allowing more HSPC cell divisions to occur.  Enhanced cxcl8/cxcr1 signaling was associated with an increase in the volume of the CHT and induction of cxcl12a expression  favoring HSPC colonization.  Finally  using parabiotic zebrafish  we show that cxcr1 acts stem cell non autonomously to improve the efficiency of donor HSPC engraftment.  This work identifies a mechanism by which the hematopoietic niche remodels to promote HSPC engraftment and suggests that cxcl8/cxcr1 signaling is a potential therapeutic target in patients undergoing hematopoietic stem cell transplantation. Overall design: Kdrl:mcherry and kdrl:mcherry;kdrl:cxcr1 zebrafish were dissociated and endothelial cells purified by FACS.  RNA seq libraries were prepared from endothelial cells purified from two independent clutches of fish four libraries total.", "parent bioproject:PRJNA358001", "pubmed:28351983", null, "kdrl:cxcr1 clutch2", "GSM2432103", null, "tissue:endothelial cells|cell type:endothelial cells", "kdrl:cxcr1 clutch2", "Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using cutadapt  then mapped to Ensembl GRCz10 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz10 Supplementary files format and content: excel files include RPKM values for each Sample", "endothelial cells", null, "Freshly sorted cells were lysed in Trizol LS and total RNA was extracted by isopropanol precipitation. Libraries were prepared using the SMARTer Universal Low Input RNA kit followed by the Low Input Library Prep Kit for Illumina Clontech Laboratories.", "Zebrafish embryos were grown under standard conditions in a 28 degree incubator.", "cell type:endothelial cells", "GSM2432103", "GSM2432103: kdrl:cxcr1 clutch2; Danio rerio; RNA Seq", "GSM2432103", null, "1", "Freshly sorted cells were lysed in Trizol LS and total RNA was extracted by isopropanol precipitation. Libraries were prepared using the SMARTer Universal Low Input RNA kit followed by the Low Input Library Prep Kit for Illumina Clontech Laboratories.", "GEO Accession:GSM2432103", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP095331", null, null, "BB-IL8-5_GCCAAT_R1.fastq.gz BB-IL8-5_GCCAAT_R2.fastq.gz", "fastq fastq", 4575871400.0, 22879357.0, "GSM2432103 r1", "0:100 1:100", "A:1212272291;C:1077863805;G:1079802103;T:1205507838;N:425363", 100, 100, null, null, 1212272291, 1077863805, 1079802103, 1205507838, 425363, "SRX2435199", "SRS1870196", "SRA505250", "GEO", "Oncology/Hematology, Boston Children's Hospital", 2, 0.79788, 0.79581, 0.25639, 0.25339, 0.74888, 0.75195, 0.55512, 0.56401, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "random_priming", "smarter", "bulk", "unknown", "unknown", null, "United States", "2016-12-19", "Undetermined", "Embryo", "Endothelium", "Cardiovascular System"], [41684, "SRR5119923", "SRX2435198", "SRS1870193", "SRP095331", "PRJNA358009", "CXCL8 and CXCR1 Remodel the Vascular Niche to Promote Hematopoietic Stem and Progenitor Cell Colonization and Engraftment [wt vs kdrl:cxcr1]", "GSE92542", "Transcriptome Analysis", "The microenvironment is an important regulator of hematopoietic stem and progenitor cell HSPC biology.  Interactions between the niche and stem cells have been difficult to track  but recent advances marking fluorescent HSPCs have allowed exquisite visualization in the caudal hematopoietic tissue CHT of the developing zebrafish.  Sinusoidal endothelial cells interact closely with HSPCs as they colonize this niche.  Here we show that the chemokine cxcl8 and its receptor  cxcr1  are abundantly expressed by zebrafish endothelial cells and we identify cxcl8/cxcr1 signaling as a positive regulator of HSPC colonization using genetic gain  and loss of function techniques.  Single cell tracking experiments demonstrated that this effect is due to an increase in HSPC \u201ccuddling\u201d by endothelial cells  thereby increasing CHT residency time and allowing more HSPC cell divisions to occur.  Enhanced cxcl8/cxcr1 signaling was associated with an increase in the volume of the CHT and induction of cxcl12a expression  favoring HSPC colonization.  Finally  using parabiotic zebrafish  we show that cxcr1 acts stem cell non autonomously to improve the efficiency of donor HSPC engraftment.  This work identifies a mechanism by which the hematopoietic niche remodels to promote HSPC engraftment and suggests that cxcl8/cxcr1 signaling is a potential therapeutic target in patients undergoing hematopoietic stem cell transplantation. Overall design: Kdrl:mcherry and kdrl:mcherry;kdrl:cxcr1 zebrafish were dissociated and endothelial cells purified by FACS.  RNA seq libraries were prepared from endothelial cells purified from two independent clutches of fish four libraries total.", "parent bioproject:PRJNA358001", "pubmed:28351983", null, "kdrl:cxcr1 clutch1", "GSM2432102", null, "tissue:endothelial cells|cell type:endothelial cells", "kdrl:cxcr1 clutch1", "Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence using cutadapt  then mapped to Ensembl GRCz10 whole genome using Tophat 2.0.11 without xxx splicing form calls Transcript abundance and differential expression were calculated with Cufflinks 2.2.1. FPKM values were used to normalize and quantify each transcripts Genome build: GRCz10 Supplementary files format and content: excel files include RPKM values for each Sample", "endothelial cells", null, "Freshly sorted cells were lysed in Trizol LS and total RNA was extracted by isopropanol precipitation. 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Libraries were prepared using the SMARTer Universal Low Input RNA kit followed by the Low Input Library Prep Kit for Illumina Clontech Laboratories.", "GEO Accession:GSM2432102", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP095331", null, null, "BB-IL8-1_ATCACG_R1.fastq.gz BB-IL8-1_ATCACG_R2.fastq.gz", "fastq fastq", 5384509000.0, 26922545.0, "GSM2432102 r1", "0:100 1:100", "A:1457197772;C:1237507818;G:1239484699;T:1449819489;N:499222", 100, 100, null, null, 1457197772, 1237507818, 1239484699, 1449819489, 499222, "SRX2435198", "SRS1870193", "SRA505250", "GEO", "Oncology/Hematology, Boston Children's Hospital", 2, 0.80446, 0.79238, 0.24797, 0.24691, 0.72423, 0.72681, 0.57301, 0.46021, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "random_priming", "smarter", "bulk", "unknown", "unknown", null, "United States", "2016-12-19", "Undetermined", "Embryo", "Endothelium", "Cardiovascular System"], [41827, "SRR5251446", "SRX2557171", "SRS1974564", "SRP099466", "PRJNA374579", "microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos", "PRJNA374579", "Other", "Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.", null, null, null, "QuantSeq mutant miRNAs   WT miR139 B1", "nicoli mutmir AG01645", null, "strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 139|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "QuantSeq mutant miRNAs   WT miR139 B1", "AG01645.1", "AG01645.1", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP099466", null, null, "AG01645.1_R1.fastq.gz", "fastq", 1574284140.0, 20714265.0, "AG01645.1 R1.fastq.gz", "0:76", "A:485471345;C:270854124;G:374164721;T:443766613;N:27337", 76, null, null, null, 485471345, 270854124, 374164721, 443766613, 27337, "SRX2557171", "SRS1974564", "SRA537606", "Yale University|Genetics", "Yale University", 1, 0.82142, null, 0.14068, null, 0.8002, null, 0.5444, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2017-03-27", "Undetermined", "Embryo", "Endothelium", "Cardiovascular System"], [41828, "SRR5251445", "SRX2557170", "SRS1974563", "SRP099466", "PRJNA374579", "microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos", "PRJNA374579", "Other", "Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. 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How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.", null, null, null, "QuantSeq mutant miRNAs   WT miR139 B3", "nicoli mutmir AG01647", null, "strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 139|replicate:3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "QuantSeq mutant miRNAs   WT miR139 B3", "AG01647.1", "AG01647.1", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP099466", null, null, "AG01647.1_R1.fastq.gz", "fastq", 881298660.0, 11596035.0, "AG01647.1 R1.fastq.gz", "0:76", "A:270675838;C:160127586;G:228157662;T:222301246;N:36328", 76, null, null, null, 270675838, 160127586, 228157662, 222301246, 36328, "SRX2557169", "SRS1974562", "SRA537606", "Yale University|Genetics", "Yale University", 1, 0.76133, null, 0.15034, null, 0.83341, null, 0.56596, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Undetermined", "Embryo", "Endothelium", "Cardiovascular System"], [41830, "SRR5251443", "SRX2557168", "SRS1974561", "SRP099466", "PRJNA374579", "microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos", "PRJNA374579", "Other", "Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.", null, null, null, "QuantSeq mutant miRNAs   Mut miR139 B1", "nicoli mutmir AG01648", null, "strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 139 ya302/ya302|molecule:mRNA|condition:miR 139|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "QuantSeq mutant miRNAs   Mut miR139 B1", "AG01648.1", "AG01648.1", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP099466", null, null, "AG01648.1_R1.fastq.gz", "fastq", 637896880.0, 8393380.0, "AG01648.1 R1.fastq.gz", "0:76", "A:192829278;C:112701153;G:153321271;T:179019095;N:26083", 76, null, null, null, 192829278, 112701153, 153321271, 179019095, 26083, "SRX2557168", "SRS1974561", "SRA537606", "Yale University|Genetics", "Yale University", 1, 0.75971, null, 0.1181, null, 0.82171, null, 0.56797, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Undetermined", "Embryo", "Endothelium", "Cardiovascular System"], [41831, "SRR5251442", "SRX2557167", "SRS1974560", "SRP099466", "PRJNA374579", "microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos", "PRJNA374579", "Other", "Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.", null, null, null, "QuantSeq mutant miRNAs   Mut miR139 B2", "nicoli mutmir AG01649", null, "strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 139 ya302/ya302|molecule:mRNA|condition:miR 139|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "QuantSeq mutant miRNAs   Mut miR139 B2", "AG01649.1", "AG01649.1", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP099466", null, null, "AG01649.1_R1.fastq.gz", "fastq", 849868328.0, 11182478.0, "AG01649.1 R1.fastq.gz", "0:76", "A:258225905;C:148467172;G:205165181;T:237974100;N:35970", 76, null, null, null, 258225905, 148467172, 205165181, 237974100, 35970, "SRX2557167", "SRS1974560", "SRA537606", "Yale University|Genetics", "Yale University", 1, 0.75096, null, 0.14506, null, 0.81507, null, 0.5545, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Undetermined", "Embryo", "Endothelium", "Cardiovascular System"], [41832, "SRR5251441", "SRX2557166", "SRS1974559", "SRP099466", "PRJNA374579", "microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos", "PRJNA374579", "Other", "Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.", null, null, null, "QuantSeq mutant miRNAs   Mut miR139 B3", "nicoli mutmir AG01650", null, "strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 139 ya302/ya302|molecule:mRNA|condition:miR 139|replicate:3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "QuantSeq mutant miRNAs   Mut miR139 B3", "AG01650.1", "AG01650.1", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP099466", null, null, "AG01650.1_R1.fastq.gz", "fastq", 998464668.0, 13137693.0, "AG01650.1 R1.fastq.gz", "0:76", "A:311526420;C:176545041;G:251852786;T:258497630;N:42791", 76, null, null, null, 311526420, 176545041, 251852786, 258497630, 42791, "SRX2557166", "SRS1974559", "SRA537606", "Yale University|Genetics", "Yale University", 1, 0.76479, null, 0.11192, null, 0.82674, null, 0.54621, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Undetermined", "Embryo", "Endothelium", "Cardiovascular System"], [41833, "SRR5251440", "SRX2557165", "SRS1974558", "SRP099466", "PRJNA374579", "microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos", "PRJNA374579", "Other", "Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.", null, null, null, "QuantSeq mutant miRNAs   WT miR24 B1", "nicoli mutmir AG01651", null, "strain:TU/AB|age:51.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 24|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "QuantSeq mutant miRNAs   WT miR24 B1", "AG01651.1", "AG01651.1", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP099466", null, null, "AG01651.1_R1.fastq.gz", "fastq", 570492252.0, 7506477.0, "AG01651.1 R1.fastq.gz", "0:76", "A:162512811;C:104071716;G:135730697;T:168149427;N:27601", 76, null, null, null, 162512811, 104071716, 135730697, 168149427, 27601, "SRX2557165", "SRS1974558", "SRA537606", "Yale University|Genetics", "Yale University", 1, 0.73988, null, 0.10157, null, 0.86647, null, 0.54252, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Undetermined", "Embryo", "Endothelium", "Cardiovascular System"], [41834, "SRR5251439", "SRX2557164", "SRS1974557", "SRP099466", "PRJNA374579", "microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos", "PRJNA374579", "Other", "Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.", null, null, null, "QuantSeq mutant miRNAs   WT miR24 B2", "nicoli mutmir AG01652", null, "strain:TU/AB|age:51.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 24|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "QuantSeq mutant miRNAs   WT miR24 B2", "AG01652.1", "AG01652.1", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP099466", null, null, "AG01652.1_R1.fastq.gz", "fastq", 1072886148.0, 14116923.0, "AG01652.1 R1.fastq.gz", "0:76", "A:338399596;C:192703439;G:242960887;T:298769761;N:52465", 76, null, null, null, 338399596, 192703439, 242960887, 298769761, 52465, "SRX2557164", "SRS1974557", "SRA537606", "Yale University|Genetics", "Yale University", 1, 0.76456, null, 0.11024, null, 0.89197, null, 0.59214, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Undetermined", "Embryo", "Endothelium", "Cardiovascular System"], [41835, "SRR5251438", "SRX2557163", "SRS1974556", "SRP099466", "PRJNA374579", "microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos", "PRJNA374579", "Other", "Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.", null, null, null, "QuantSeq mutant miRNAs   WT miR24 B3", "nicoli mutmir AG01653", null, "strain:TU/AB|age:51.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 24|replicate:3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "QuantSeq mutant miRNAs   WT miR24 B3", "AG01653.1", "AG01653.1", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP099466", null, null, "AG01653.1_R1.fastq.gz", "fastq", 1016374144.0, 13373344.0, "AG01653.1 R1.fastq.gz", "0:76", "A:310958343;C:168702106;G:223420046;T:313241363;N:52286", 76, null, null, null, 310958343, 168702106, 223420046, 313241363, 52286, "SRX2557163", "SRS1974556", "SRA537606", "Yale University|Genetics", "Yale University", 1, 0.75735, null, 0.12224, null, 0.79756, null, 0.55136, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2017-02-13", "Undetermined", "Embryo", "Endothelium", "Cardiovascular System"], [41836, "SRR5251437", "SRX2557162", "SRS1974555", "SRP099466", "PRJNA374579", "microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos", "PRJNA374579", "Other", "Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.", null, null, null, "QuantSeq mutant miRNAs   Mut miR24 B1", "nicoli mutmir AG01654", null, "strain:TU/AB|age:51.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 24 ya324/? ya325/? ya326/? ya327/?|molecule:mRNA|condition:miR 24|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "QuantSeq mutant miRNAs   Mut miR24 B1", "AG01654.1", "AG01654.1", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP099466", null, null, "AG01654.1_R1.fastq.gz", "fastq", 782170112.0, 10291712.0, "AG01654.1 R1.fastq.gz", "0:76", "A:238316720;C:132163709;G:179301544;T:232350598;N:37541", 76, null, null, null, 238316720, 132163709, 179301544, 232350598, 37541, "SRX2557162", "SRS1974555", "SRA537606", "Yale University|Genetics", "Yale University", 1, 0.7683, null, 0.10712, null, 0.80034, null, 0.55804, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Undetermined", "Embryo", "Endothelium", "Cardiovascular System"], [41837, "SRR5251436", "SRX2557161", "SRS1974554", "SRP099466", "PRJNA374579", "microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos", "PRJNA374579", "Other", "Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.", null, null, null, "QuantSeq mutant miRNAs   Mut miR24 B2", "nicoli mutmir AG01655", null, "strain:TU/AB|age:51.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 24 ya324/? ya325/? ya326/? ya327/?|molecule:mRNA|condition:miR 24|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "QuantSeq mutant miRNAs   Mut miR24 B2", "AG01655.1", "AG01655.1", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP099466", null, null, "AG01655.1_R1.fastq.gz", "fastq", 1053946340.0, 13867715.0, "AG01655.1 R1.fastq.gz", "0:76", "A:318351311;C:191163031;G:240348413;T:304030367;N:53218", 76, null, null, null, 318351311, 191163031, 240348413, 304030367, 53218, "SRX2557161", "SRS1974554", "SRA537606", "Yale University|Genetics", "Yale University", 1, 0.77588, null, 0.07983, null, 0.83934, null, 0.56228, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Undetermined", "Embryo", "Endothelium", "Cardiovascular System"], [41838, "SRR5251435", "SRX2557160", "SRS1974553", "SRP099466", "PRJNA374579", "microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos", "PRJNA374579", "Other", "Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.", null, null, null, "QuantSeq mutant miRNAs   Mut miR24 B3", "nicoli mutmir AG01656", null, "strain:TU/AB|age:51.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 24 ya324/? ya325/? ya326/? ya327/?|molecule:mRNA|condition:miR 24|replicate:3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "QuantSeq mutant miRNAs   Mut miR24 B3", "AG01656.1", "AG01656.1", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP099466", null, null, "AG01656.1_R1.fastq.gz", "fastq", 1182467736.0, 15558786.0, "AG01656.1 R1.fastq.gz", "0:76", "A:344465226;C:204677242;G:269228338;T:364036735;N:60195", 76, null, null, null, 344465226, 204677242, 269228338, 364036735, 60195, "SRX2557160", "SRS1974553", "SRA537606", "Yale University|Genetics", "Yale University", 1, 0.78956, null, 0.13495, null, 0.81517, null, 0.56342, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2017-02-13", "Undetermined", "Embryo", "Endothelium", "Cardiovascular System"], [41839, "SRR5251434", "SRX2557159", "SRS1974552", "SRP099466", "PRJNA374579", "microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos", "PRJNA374579", "Other", "Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.", null, null, null, "QuantSeq mutant miRNAs   WT miR223 B1", "nicoli mutmir AG01657", null, "strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 223|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "QuantSeq mutant miRNAs   WT miR223 B1", "AG01657.1", "AG01657.1", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP099466", null, null, "AG01657.1_R1.fastq.gz", "fastq", 536336712.0, 7057062.0, "AG01657.1 R1.fastq.gz", "0:76", "A:158301607;C:93070120;G:121382262;T:163555487;N:27236", 76, null, null, null, 158301607, 93070120, 121382262, 163555487, 27236, "SRX2557159", "SRS1974552", "SRA537606", "Yale University|Genetics", "Yale University", 1, 0.76425, null, 0.1278, null, 0.84222, null, 0.55305, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2017-02-13", "Undetermined", "Embryo", "Endothelium", "Cardiovascular System"], [41840, "SRR5251433", "SRX2557158", "SRS1974551", "SRP099466", "PRJNA374579", "microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos", "PRJNA374579", "Other", "Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.", null, null, null, "QuantSeq mutant miRNAs   WT miR223 B2", "nicoli mutmir AG01658", null, "strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 223|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "QuantSeq mutant miRNAs   WT miR223 B2", "AG01658.1", "AG01658.1", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP099466", null, null, "AG01658.1_R1.fastq.gz", "fastq", 798581856.0, 10507656.0, "AG01658.1 R1.fastq.gz", "0:76", "A:241352089;C:134327379;G:183394123;T:239469845;N:38420", 76, null, null, null, 241352089, 134327379, 183394123, 239469845, 38420, "SRX2557158", "SRS1974551", "SRA537606", "Yale University|Genetics", "Yale University", 1, 0.76221, null, 0.13398, null, 0.82459, null, 0.55228, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Undetermined", "Embryo", "Endothelium", "Cardiovascular System"], [41841, "SRR5251432", "SRX2557157", "SRS1974550", "SRP099466", "PRJNA374579", "microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos", "PRJNA374579", "Other", "Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.", null, null, null, "QuantSeq mutant miRNAs   WT miR223 B3", "nicoli mutmir AG01659", null, "strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 223|replicate:3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "QuantSeq mutant miRNAs   WT miR223 B3", "AG01659.1", "AG01659.1", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP099466", null, null, "AG01659.1_R1.fastq.gz", "fastq", 1093998948.0, 14394723.0, "AG01659.1 R1.fastq.gz", "0:76", "A:330741822;C:186325335;G:249557623;T:327320449;N:53719", 76, null, null, null, 330741822, 186325335, 249557623, 327320449, 53719, "SRX2557157", "SRS1974550", "SRA537606", "Yale University|Genetics", "Yale University", 1, 0.77108, null, 0.14674, null, 0.80955, null, 0.55819, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Undetermined", "Embryo", "Endothelium", "Cardiovascular System"], [41842, "SRR5251431", "SRX2557156", "SRS1974549", "SRP099466", "PRJNA374579", "microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos", "PRJNA374579", "Other", "Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.", null, null, null, "QuantSeq mutant miRNAs   Mut miR223 B1", "nicoli mutmir AG01660", null, "strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 223 ya304/ya304|molecule:mRNA|condition:miR 223|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "QuantSeq mutant miRNAs   Mut miR223 B1", "AG01660.1", "AG01660.1", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP099466", null, null, "AG01660.1_R1.fastq.gz", "fastq", 849905492.0, 11182967.0, "AG01660.1 R1.fastq.gz", "0:76", "A:250953875;C:146191904;G:190040699;T:262674911;N:44103", 76, null, null, null, 250953875, 146191904, 190040699, 262674911, 44103, "SRX2557156", "SRS1974549", "SRA537606", "Yale University|Genetics", "Yale University", 1, 0.7687, null, 0.14192, null, 0.82842, null, 0.5344, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2017-02-13", "Undetermined", "Embryo", "Endothelium", "Cardiovascular System"], [41843, "SRR5251430", "SRX2557155", "SRS1974548", "SRP099466", "PRJNA374579", "microRNAs Establish Uniform Traits during the Architecture of Vertebrate Embryos", "PRJNA374579", "Other", "Proper functioning of an organism requires cells and tissues to behave in uniform  well organized ways. How this optimum of phenotypes is achieved during the development of vertebrates is unclear. Here  we carried out a multifaceted and single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single and multi gene miRNA families. We found that embryos lacking particular miRNA dependent signaling pathways develop a vascular trait similar to wild type  but with a profound increase in phenotypic heterogeneity. Aberrant trait variance in miRNA mutant embryos uniquely sensitizes their vascular system to environmental perturbations. We uncovered a previously unrecognized role for specific vertebrate miRNAs to protect tissue development against phenotypic variability. This discovery marks an important advance in our comprehension of how miRNAs function in the development of higher organisms.", null, null, null, "QuantSeq mutant miRNAs   Mut miR223 B2", "nicoli mutmir AG01661", null, "strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|genotype:miR 223 ya304/ya304|molecule:mRNA|condition:miR 223|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "QuantSeq mutant miRNAs   Mut miR223 B2", "AG01661.1", "AG01661.1", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP099466", null, null, "AG01661.1_R1.fastq.gz", "fastq", 840115400.0, 11054150.0, "AG01661.1 R1.fastq.gz", "0:76", "A:257057495;C:141775085;G:188281166;T:252960590;N:41064", 76, null, null, null, 257057495, 141775085, 188281166, 252960590, 41064, "SRX2557155", "SRS1974548", "SRA537606", "Yale University|Genetics", "Yale University", 1, 0.74292, null, 0.10759, null, 0.83615, null, 0.55136, null, 76, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "small_rna", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2017-03-28", "Undetermined", "Embryo", "Endothelium", "Cardiovascular System"], [67022, "SRR16973878", "SRX13164742", "SRS11095945", "SRP346708", "PRJNA781453", "WGBS and RNA seq of Danio rerio in HSPC generation", "GSE189072", "Other", "In this study  we interrogated the role of DNA methylation in HSPC generation by taking advantage of dnmt1 knockout/knockdown embryos in zebrafish. First  we generated a comprehensive DNA methylation landscape of EHT  which revealed gradually hypermethylated regions associated with vasculogenesis. Taking advantage of dnmt1 deficient embryos  we showed that the decreased DNA methylation blocked HSPC emergence. Mechanistically  we demonstrated that the decreased DNA methylation increased the expression of arterial genes and Notch signaling  thus contributing to defects in the EHT in dnmt1 deficient embryos. Herein  we identified that DNA methylation  as epigenetic regulator  participates in the negative modulation of Notch signaling through inhibiting transcription during HSPC generation in zebrafish. Overall design: WGBS and RNA seq of Danio rerio in EC HE and HSPC.", null, "pubmed:35502759", null, "HE mut rep3 RNA", "GSM5694252", null, "tissue:hemogenic endothelium cells|developmental stage:HE|genotype:dnmt1 mutant|region:AGM", "HE mut rep3 RNA", "Basecalls perfomed using CASAVA2.19 WGBS and RNA seq raw sequencing reads were first trimmed for adapter and low quality sequences. Then mapped to GRCz11 using BS Seeker2v2.1.8 and hisat2v2.2.1 with parameters \" t Y  m 0.04   bt2  end to end\" and \"  known splicesite infile  p 30  k 10   dta  t\" separately. Student's T test was used to perform DMR analysis for WGBS data. Gene expression level was quantified by HTSeqv0.12.4 and differentially expressed genesDEGs were determined by DESeq2v1.30.1 Genome build: GRCz11 Supplementary files format and content: RNA seq raw count matrix Supplementary files format and content: raw count.txt raw counts Supplementary files format and content: EC sib.bed DMRs of  EC sibling compared with HE sibling and HSC sibling Supplementary files format and content: HE sib.bed DMRs of  HE sibling compared with EC sibling and HSC sibling Supplementary files format and content: HSC sib.bed DMRs of  HSC sibling compared with EC sibling and HE sibling Supplementary files format and content: EC HE sib.bed DMRs of  EC and HE sibling Supplementary files format and content: HE HSC sib.bed DMRs of  HE and HSC sibling Supplementary files format and content: EC sib mut.bed DMRs of  EC sibling and EC mutant Supplementary files format and content: HE sib mut.bed DMRs of  HE sibling and HE mutant Supplementary files format and content: HSC sib mut.bed DMRs of  HSC sibling and HSC mutant", "hemogenic endothelium cells", null, "Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3\u2032 biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification", null, "developmental stage:HE|genotype:dnmt1 mutant|region:AGM", "GSM5694252", "GSM5694252: HE mut rep3 RNA; Danio rerio; RNA Seq", "GSM5694252", null, "1", "Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3\u2032 biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification", "GEO Accession:GSM5694252", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP346708", null, "loader:fastq load.py", "HE_sib_3_1_RNA.fq.gz HE_sib_3_2_RNA.fq.gz", "fastq fastq", 8484093900.0, 28280313.0, "GSM5694252 r1", "0:150 1:150", "A:2396956113;C:1725799170;G:1832630297;T:2528680586;N:27734", 150, 150, null, null, 2396956113, 1725799170, 1832630297, 2528680586, 27734, "SRX13164742", "SRS11095945", "SRA1331007", "GEO", "Institute of Hematology and Blood Diseases Hospital", 2, 0.93895, 0.93325, 0.16467, 0.16385, 0.76595, 0.76895, 0.47613, 0.46536, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "strtseq", null, "China", "2021-11-18", "Undetermined", "Embryo", "Endothelium", "Cardiovascular System"], [67023, "SRR16973877", "SRX13164741", "SRS11095944", "SRP346708", "PRJNA781453", "WGBS and RNA seq of Danio rerio in HSPC generation", "GSE189072", "Other", "In this study  we interrogated the role of DNA methylation in HSPC generation by taking advantage of dnmt1 knockout/knockdown embryos in zebrafish. First  we generated a comprehensive DNA methylation landscape of EHT  which revealed gradually hypermethylated regions associated with vasculogenesis. Taking advantage of dnmt1 deficient embryos  we showed that the decreased DNA methylation blocked HSPC emergence. Mechanistically  we demonstrated that the decreased DNA methylation increased the expression of arterial genes and Notch signaling  thus contributing to defects in the EHT in dnmt1 deficient embryos. Herein  we identified that DNA methylation  as epigenetic regulator  participates in the negative modulation of Notch signaling through inhibiting transcription during HSPC generation in zebrafish. Overall design: WGBS and RNA seq of Danio rerio in EC HE and HSPC.", null, "pubmed:35502759", null, "HE mut rep2 RNA", "GSM5694251", null, "tissue:hemogenic endothelium cells|developmental stage:HE|genotype:dnmt1 mutant|region:AGM", "HE mut rep2 RNA", "Basecalls perfomed using CASAVA2.19 WGBS and RNA seq raw sequencing reads were first trimmed for adapter and low quality sequences. Then mapped to GRCz11 using BS Seeker2v2.1.8 and hisat2v2.2.1 with parameters \" t Y  m 0.04   bt2  end to end\" and \"  known splicesite infile  p 30  k 10   dta  t\" separately. Student's T test was used to perform DMR analysis for WGBS data. Gene expression level was quantified by HTSeqv0.12.4 and differentially expressed genesDEGs were determined by DESeq2v1.30.1 Genome build: GRCz11 Supplementary files format and content: RNA seq raw count matrix Supplementary files format and content: raw count.txt raw counts Supplementary files format and content: EC sib.bed DMRs of  EC sibling compared with HE sibling and HSC sibling Supplementary files format and content: HE sib.bed DMRs of  HE sibling compared with EC sibling and HSC sibling Supplementary files format and content: HSC sib.bed DMRs of  HSC sibling compared with EC sibling and HE sibling Supplementary files format and content: EC HE sib.bed DMRs of  EC and HE sibling Supplementary files format and content: HE HSC sib.bed DMRs of  HE and HSC sibling Supplementary files format and content: EC sib mut.bed DMRs of  EC sibling and EC mutant Supplementary files format and content: HE sib mut.bed DMRs of  HE sibling and HE mutant Supplementary files format and content: HSC sib mut.bed DMRs of  HSC sibling and HSC mutant", "hemogenic endothelium cells", null, "Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3\u2032 biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification", null, "developmental stage:HE|genotype:dnmt1 mutant|region:AGM", "GSM5694251", "GSM5694251: HE mut rep2 RNA; Danio rerio; RNA Seq", "GSM5694251", null, "1", "Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3\u2032 biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification", "GEO Accession:GSM5694251", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP346708", null, null, "HE_sib_2_1_RNA.fq.gz HE_sib_2_2_RNA.fq.gz", "fastq fastq", 3391937700.0, 11306459.0, "GSM5694251 r1", "0:150 1:150", "A:981400300;C:664246146;G:716019213;T:1030238113;N:33928", 150, 150, null, null, 981400300, 664246146, 716019213, 1030238113, 33928, "SRX13164741", "SRS11095944", "SRA1331007", "GEO", "Institute of Hematology and Blood Diseases Hospital", 2, 0.88669, 0.88216, 0.25368, 0.25155, 0.76361, 0.76883, 0.54578, 0.54556, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "strtseq", null, "China", "2021-11-18", "Undetermined", "Embryo", "Endothelium", "Cardiovascular System"], [67024, "SRR16973876", "SRX13164740", "SRS11095942", "SRP346708", "PRJNA781453", "WGBS and RNA seq of Danio rerio in HSPC generation", "GSE189072", "Other", "In this study  we interrogated the role of DNA methylation in HSPC generation by taking advantage of dnmt1 knockout/knockdown embryos in zebrafish. First  we generated a comprehensive DNA methylation landscape of EHT  which revealed gradually hypermethylated regions associated with vasculogenesis. Taking advantage of dnmt1 deficient embryos  we showed that the decreased DNA methylation blocked HSPC emergence. Mechanistically  we demonstrated that the decreased DNA methylation increased the expression of arterial genes and Notch signaling  thus contributing to defects in the EHT in dnmt1 deficient embryos. Herein  we identified that DNA methylation  as epigenetic regulator  participates in the negative modulation of Notch signaling through inhibiting transcription during HSPC generation in zebrafish. Overall design: WGBS and RNA seq of Danio rerio in EC HE and HSPC.", null, "pubmed:35502759", null, "HE mut rep1 RNA", "GSM5694250", null, "tissue:hemogenic endothelium cells|developmental stage:HE|genotype:dnmt1 mutant|region:AGM", "HE mut rep1 RNA", "Basecalls perfomed using CASAVA2.19 WGBS and RNA seq raw sequencing reads were first trimmed for adapter and low quality sequences. Then mapped to GRCz11 using BS Seeker2v2.1.8 and hisat2v2.2.1 with parameters \" t Y  m 0.04   bt2  end to end\" and \"  known splicesite infile  p 30  k 10   dta  t\" separately. Student's T test was used to perform DMR analysis for WGBS data. Gene expression level was quantified by HTSeqv0.12.4 and differentially expressed genesDEGs were determined by DESeq2v1.30.1 Genome build: GRCz11 Supplementary files format and content: RNA seq raw count matrix Supplementary files format and content: raw count.txt raw counts Supplementary files format and content: EC sib.bed DMRs of  EC sibling compared with HE sibling and HSC sibling Supplementary files format and content: HE sib.bed DMRs of  HE sibling compared with EC sibling and HSC sibling Supplementary files format and content: HSC sib.bed DMRs of  HSC sibling compared with EC sibling and HE sibling Supplementary files format and content: EC HE sib.bed DMRs of  EC and HE sibling Supplementary files format and content: HE HSC sib.bed DMRs of  HE and HSC sibling Supplementary files format and content: EC sib mut.bed DMRs of  EC sibling and EC mutant Supplementary files format and content: HE sib mut.bed DMRs of  HE sibling and HE mutant Supplementary files format and content: HSC sib mut.bed DMRs of  HSC sibling and HSC mutant", "hemogenic endothelium cells", null, "Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3\u2032 biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification", null, "developmental stage:HE|genotype:dnmt1 mutant|region:AGM", "GSM5694250", "GSM5694250: HE mut rep1 RNA; Danio rerio; RNA Seq", "GSM5694250", null, "1", "Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3\u2032 biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification", "GEO Accession:GSM5694250", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP346708", null, null, "HE_sib_1_1_RNA.fq.gz HE_sib_1_2_RNA.fq.gz", "fastq fastq", 3246930300.0, 10823101.0, "GSM5694250 r1", "0:150 1:150", "A:938425919;C:639911754;G:671817291;T:996741337;N:33999", 150, 150, null, null, 938425919, 639911754, 671817291, 996741337, 33999, "SRX13164740", "SRS11095942", "SRA1331007", "GEO", "Institute of Hematology and Blood Diseases Hospital", 2, 0.93431, 0.92139, 0.18855, 0.18424, 0.78886, 0.79308, 0.52892, 0.52798, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "strtseq", null, "China", "2021-11-18", "Undetermined", "Embryo", "Endothelium", "Cardiovascular System"], [67025, "SRR16973875", "SRX13164739", "SRS11095943", "SRP346708", "PRJNA781453", "WGBS and RNA seq of Danio rerio in HSPC generation", "GSE189072", "Other", "In this study  we interrogated the role of DNA methylation in HSPC generation by taking advantage of dnmt1 knockout/knockdown embryos in zebrafish. First  we generated a comprehensive DNA methylation landscape of EHT  which revealed gradually hypermethylated regions associated with vasculogenesis. Taking advantage of dnmt1 deficient embryos  we showed that the decreased DNA methylation blocked HSPC emergence. Mechanistically  we demonstrated that the decreased DNA methylation increased the expression of arterial genes and Notch signaling  thus contributing to defects in the EHT in dnmt1 deficient embryos. Herein  we identified that DNA methylation  as epigenetic regulator  participates in the negative modulation of Notch signaling through inhibiting transcription during HSPC generation in zebrafish. Overall design: WGBS and RNA seq of Danio rerio in EC HE and HSPC.", null, "pubmed:35502759", null, "HE sib rep3 RNA", "GSM5694249", null, "tissue:hemogenic endothelium cells|developmental stage:HE|genotype:sibling|region:AGM", "HE sib rep3 RNA", "Basecalls perfomed using CASAVA2.19 WGBS and RNA seq raw sequencing reads were first trimmed for adapter and low quality sequences. Then mapped to GRCz11 using BS Seeker2v2.1.8 and hisat2v2.2.1 with parameters \" t Y  m 0.04   bt2  end to end\" and \"  known splicesite infile  p 30  k 10   dta  t\" separately. Student's T test was used to perform DMR analysis for WGBS data. Gene expression level was quantified by HTSeqv0.12.4 and differentially expressed genesDEGs were determined by DESeq2v1.30.1 Genome build: GRCz11 Supplementary files format and content: RNA seq raw count matrix Supplementary files format and content: raw count.txt raw counts Supplementary files format and content: EC sib.bed DMRs of  EC sibling compared with HE sibling and HSC sibling Supplementary files format and content: HE sib.bed DMRs of  HE sibling compared with EC sibling and HSC sibling Supplementary files format and content: HSC sib.bed DMRs of  HSC sibling compared with EC sibling and HE sibling Supplementary files format and content: EC HE sib.bed DMRs of  EC and HE sibling Supplementary files format and content: HE HSC sib.bed DMRs of  HE and HSC sibling Supplementary files format and content: EC sib mut.bed DMRs of  EC sibling and EC mutant Supplementary files format and content: HE sib mut.bed DMRs of  HE sibling and HE mutant Supplementary files format and content: HSC sib mut.bed DMRs of  HSC sibling and HSC mutant", "hemogenic endothelium cells", null, "Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3\u2032 biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification", null, "developmental stage:HE|genotype:sibling|region:AGM", "GSM5694249", "GSM5694249: HE sib rep3 RNA; Danio rerio; RNA Seq", "GSM5694249", null, "1", "Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3\u2032 biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification", "GEO Accession:GSM5694249", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP346708", null, "loader:fastq load.py", "HE_mut_3_1_RNA.fq.gz HE_mut_3_2_RNA.fq.gz", "fastq fastq", 7531062600.0, 25103542.0, "GSM5694249 r1", "0:150 1:150", "A:2130133337;C:1522023953;G:1620977746;T:2257902956;N:24608", 150, 150, null, null, 2130133337, 1522023953, 1620977746, 2257902956, 24608, "SRX13164739", "SRS11095943", "SRA1331007", "GEO", "Institute of Hematology and Blood Diseases Hospital", 2, 0.93514, 0.92906, 0.1645, 0.16366, 0.76706, 0.77086, 0.4871, 0.48732, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "strtseq", null, "China", "2021-11-18", "Undetermined", "Embryo", "Endothelium", "Cardiovascular System"], [67026, "SRR16973874", "SRX13164738", "SRS11095941", "SRP346708", "PRJNA781453", "WGBS and RNA seq of Danio rerio in HSPC generation", "GSE189072", "Other", "In this study  we interrogated the role of DNA methylation in HSPC generation by taking advantage of dnmt1 knockout/knockdown embryos in zebrafish. First  we generated a comprehensive DNA methylation landscape of EHT  which revealed gradually hypermethylated regions associated with vasculogenesis. Taking advantage of dnmt1 deficient embryos  we showed that the decreased DNA methylation blocked HSPC emergence. Mechanistically  we demonstrated that the decreased DNA methylation increased the expression of arterial genes and Notch signaling  thus contributing to defects in the EHT in dnmt1 deficient embryos. Herein  we identified that DNA methylation  as epigenetic regulator  participates in the negative modulation of Notch signaling through inhibiting transcription during HSPC generation in zebrafish. Overall design: WGBS and RNA seq of Danio rerio in EC HE and HSPC.", null, "pubmed:35502759", null, "HE sib rep2 RNA", "GSM5694248", null, "tissue:hemogenic endothelium cells|developmental stage:HE|genotype:sibling|region:AGM", "HE sib rep2 RNA", "Basecalls perfomed using CASAVA2.19 WGBS and RNA seq raw sequencing reads were first trimmed for adapter and low quality sequences. Then mapped to GRCz11 using BS Seeker2v2.1.8 and hisat2v2.2.1 with parameters \" t Y  m 0.04   bt2  end to end\" and \"  known splicesite infile  p 30  k 10   dta  t\" separately. Student's T test was used to perform DMR analysis for WGBS data. Gene expression level was quantified by HTSeqv0.12.4 and differentially expressed genesDEGs were determined by DESeq2v1.30.1 Genome build: GRCz11 Supplementary files format and content: RNA seq raw count matrix Supplementary files format and content: raw count.txt raw counts Supplementary files format and content: EC sib.bed DMRs of  EC sibling compared with HE sibling and HSC sibling Supplementary files format and content: HE sib.bed DMRs of  HE sibling compared with EC sibling and HSC sibling Supplementary files format and content: HSC sib.bed DMRs of  HSC sibling compared with EC sibling and HE sibling Supplementary files format and content: EC HE sib.bed DMRs of  EC and HE sibling Supplementary files format and content: HE HSC sib.bed DMRs of  HE and HSC sibling Supplementary files format and content: EC sib mut.bed DMRs of  EC sibling and EC mutant Supplementary files format and content: HE sib mut.bed DMRs of  HE sibling and HE mutant Supplementary files format and content: HSC sib mut.bed DMRs of  HSC sibling and HSC mutant", "hemogenic endothelium cells", null, "Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3\u2032 biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification", null, "developmental stage:HE|genotype:sibling|region:AGM", "GSM5694248", "GSM5694248: HE sib rep2 RNA; Danio rerio; RNA Seq", "GSM5694248", null, "1", "Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3\u2032 biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification", "GEO Accession:GSM5694248", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP346708", null, null, "HE_mut_2_1_RNA.fq.gz HE_mut_2_2_RNA.fq.gz", "fastq fastq", 3480792300.0, 11602641.0, "GSM5694248 r1", "0:150 1:150", "A:992011776;C:688862509;G:749973391;T:1049913481;N:31143", 150, 150, null, null, 992011776, 688862509, 749973391, 1049913481, 31143, "SRX13164738", "SRS11095941", "SRA1331007", "GEO", "Institute of Hematology and Blood Diseases Hospital", 2, 0.92794, 0.92305, 0.17775, 0.17805, 0.77159, 0.77705, 0.51315, 0.52162, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "strtseq", null, "China", "2021-11-18", "Undetermined", "Embryo", "Endothelium", "Cardiovascular System"], [67027, "SRR16973873", "SRX13164737", "SRS11095940", "SRP346708", "PRJNA781453", "WGBS and RNA seq of Danio rerio in HSPC generation", "GSE189072", "Other", "In this study  we interrogated the role of DNA methylation in HSPC generation by taking advantage of dnmt1 knockout/knockdown embryos in zebrafish. First  we generated a comprehensive DNA methylation landscape of EHT  which revealed gradually hypermethylated regions associated with vasculogenesis. Taking advantage of dnmt1 deficient embryos  we showed that the decreased DNA methylation blocked HSPC emergence. Mechanistically  we demonstrated that the decreased DNA methylation increased the expression of arterial genes and Notch signaling  thus contributing to defects in the EHT in dnmt1 deficient embryos. Herein  we identified that DNA methylation  as epigenetic regulator  participates in the negative modulation of Notch signaling through inhibiting transcription during HSPC generation in zebrafish. Overall design: WGBS and RNA seq of Danio rerio in EC HE and HSPC.", null, "pubmed:35502759", null, "HE sib rep1 RNA", "GSM5694247", null, "tissue:hemogenic endothelium cells|developmental stage:HE|genotype:sibling|region:AGM", "HE sib rep1 RNA", "Basecalls perfomed using CASAVA2.19 WGBS and RNA seq raw sequencing reads were first trimmed for adapter and low quality sequences. Then mapped to GRCz11 using BS Seeker2v2.1.8 and hisat2v2.2.1 with parameters \" t Y  m 0.04   bt2  end to end\" and \"  known splicesite infile  p 30  k 10   dta  t\" separately. Student's T test was used to perform DMR analysis for WGBS data. Gene expression level was quantified by HTSeqv0.12.4 and differentially expressed genesDEGs were determined by DESeq2v1.30.1 Genome build: GRCz11 Supplementary files format and content: RNA seq raw count matrix Supplementary files format and content: raw count.txt raw counts Supplementary files format and content: EC sib.bed DMRs of  EC sibling compared with HE sibling and HSC sibling Supplementary files format and content: HE sib.bed DMRs of  HE sibling compared with EC sibling and HSC sibling Supplementary files format and content: HSC sib.bed DMRs of  HSC sibling compared with EC sibling and HE sibling Supplementary files format and content: EC HE sib.bed DMRs of  EC and HE sibling Supplementary files format and content: HE HSC sib.bed DMRs of  HE and HSC sibling Supplementary files format and content: EC sib mut.bed DMRs of  EC sibling and EC mutant Supplementary files format and content: HE sib mut.bed DMRs of  HE sibling and HE mutant Supplementary files format and content: HSC sib mut.bed DMRs of  HSC sibling and HSC mutant", "hemogenic endothelium cells", null, "Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3\u2032 biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification", null, "developmental stage:HE|genotype:sibling|region:AGM", "GSM5694247", "GSM5694247: HE sib rep1 RNA; Danio rerio; RNA Seq", "GSM5694247", null, "1", "Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3\u2032 biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification", "GEO Accession:GSM5694247", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP346708", null, null, "HE_mut_1_1_RNA.fq.gz HE_mut_1_2_RNA.fq.gz", "fastq fastq", 4147333500.0, 13824445.0, "GSM5694247 r1", "0:150 1:150", "A:1182622375;C:805503602;G:885424962;T:1273741037;N:41524", 150, 150, null, null, 1182622375, 805503602, 885424962, 1273741037, 41524, "SRX13164737", "SRS11095940", "SRA1331007", "GEO", "Institute of Hematology and Blood Diseases Hospital", 2, 0.92289, 0.91984, 0.22715, 0.22596, 0.77926, 0.78644, 0.54161, 0.53476, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "strtseq", null, "China", "2021-11-18", "Undetermined", "Embryo", "Endothelium", "Cardiovascular System"], [67028, "SRR16973872", "SRX13164736", "SRS11095939", "SRP346708", "PRJNA781453", "WGBS and RNA seq of Danio rerio in HSPC generation", "GSE189072", "Other", "In this study  we interrogated the role of DNA methylation in HSPC generation by taking advantage of dnmt1 knockout/knockdown embryos in zebrafish. First  we generated a comprehensive DNA methylation landscape of EHT  which revealed gradually hypermethylated regions associated with vasculogenesis. Taking advantage of dnmt1 deficient embryos  we showed that the decreased DNA methylation blocked HSPC emergence. Mechanistically  we demonstrated that the decreased DNA methylation increased the expression of arterial genes and Notch signaling  thus contributing to defects in the EHT in dnmt1 deficient embryos. Herein  we identified that DNA methylation  as epigenetic regulator  participates in the negative modulation of Notch signaling through inhibiting transcription during HSPC generation in zebrafish. Overall design: WGBS and RNA seq of Danio rerio in EC HE and HSPC.", null, "pubmed:35502759", null, "EC mut rep3 RNA", "GSM5694246", null, "tissue:endothelial cells|developmental stage:EC|genotype:dnmt1 mutant|region:AGM", "EC mut rep3 RNA", "Basecalls perfomed using CASAVA2.19 WGBS and RNA seq raw sequencing reads were first trimmed for adapter and low quality sequences. Then mapped to GRCz11 using BS Seeker2v2.1.8 and hisat2v2.2.1 with parameters \" t Y  m 0.04   bt2  end to end\" and \"  known splicesite infile  p 30  k 10   dta  t\" separately. Student's T test was used to perform DMR analysis for WGBS data. Gene expression level was quantified by HTSeqv0.12.4 and differentially expressed genesDEGs were determined by DESeq2v1.30.1 Genome build: GRCz11 Supplementary files format and content: RNA seq raw count matrix Supplementary files format and content: raw count.txt raw counts Supplementary files format and content: EC sib.bed DMRs of  EC sibling compared with HE sibling and HSC sibling Supplementary files format and content: HE sib.bed DMRs of  HE sibling compared with EC sibling and HSC sibling Supplementary files format and content: HSC sib.bed DMRs of  HSC sibling compared with EC sibling and HE sibling Supplementary files format and content: EC HE sib.bed DMRs of  EC and HE sibling Supplementary files format and content: HE HSC sib.bed DMRs of  HE and HSC sibling Supplementary files format and content: EC sib mut.bed DMRs of  EC sibling and EC mutant Supplementary files format and content: HE sib mut.bed DMRs of  HE sibling and HE mutant Supplementary files format and content: HSC sib mut.bed DMRs of  HSC sibling and HSC mutant", "endothelial cells", null, "Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3\u2032 biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification", null, "developmental stage:EC|genotype:dnmt1 mutant|region:AGM", "GSM5694246", "GSM5694246: EC mut rep3 RNA; Danio rerio; RNA Seq", "GSM5694246", null, "1", "Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3\u2032 biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification", "GEO Accession:GSM5694246", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP346708", null, "loader:fastq load.py", "EC_sib_3_1_RNA.fq.gz EC_sib_3_2_RNA.fq.gz", "fastq fastq", 5197238700.0, 17324129.0, "GSM5694246 r1", "0:150 1:150", "A:1518447950;C:1011812171;G:1095102019;T:1571846375;N:30185", 150, 150, null, null, 1518447950, 1011812171, 1095102019, 1571846375, 30185, "SRX13164736", "SRS11095939", "SRA1331007", "GEO", "Institute of Hematology and Blood Diseases Hospital", 2, 0.91741, 0.90997, 0.30958, 0.30583, 0.78573, 0.79243, 0.44787, 0.56503, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "strtseq", null, "China", "2021-11-18", "Undetermined", "Embryo", "Endothelium", "Cardiovascular System"], [67029, "SRR16973871", "SRX13164735", "SRS11095938", "SRP346708", "PRJNA781453", "WGBS and RNA seq of Danio rerio in HSPC generation", "GSE189072", "Other", "In this study  we interrogated the role of DNA methylation in HSPC generation by taking advantage of dnmt1 knockout/knockdown embryos in zebrafish. First  we generated a comprehensive DNA methylation landscape of EHT  which revealed gradually hypermethylated regions associated with vasculogenesis. Taking advantage of dnmt1 deficient embryos  we showed that the decreased DNA methylation blocked HSPC emergence. Mechanistically  we demonstrated that the decreased DNA methylation increased the expression of arterial genes and Notch signaling  thus contributing to defects in the EHT in dnmt1 deficient embryos. Herein  we identified that DNA methylation  as epigenetic regulator  participates in the negative modulation of Notch signaling through inhibiting transcription during HSPC generation in zebrafish. Overall design: WGBS and RNA seq of Danio rerio in EC HE and HSPC.", null, "pubmed:35502759", null, "EC mut rep2 RNA", "GSM5694245", null, "tissue:endothelial cells|developmental stage:EC|genotype:dnmt1 mutant|region:AGM", "EC mut rep2 RNA", "Basecalls perfomed using CASAVA2.19 WGBS and RNA seq raw sequencing reads were first trimmed for adapter and low quality sequences. Then mapped to GRCz11 using BS Seeker2v2.1.8 and hisat2v2.2.1 with parameters \" t Y  m 0.04   bt2  end to end\" and \"  known splicesite infile  p 30  k 10   dta  t\" separately. Student's T test was used to perform DMR analysis for WGBS data. Gene expression level was quantified by HTSeqv0.12.4 and differentially expressed genesDEGs were determined by DESeq2v1.30.1 Genome build: GRCz11 Supplementary files format and content: RNA seq raw count matrix Supplementary files format and content: raw count.txt raw counts Supplementary files format and content: EC sib.bed DMRs of  EC sibling compared with HE sibling and HSC sibling Supplementary files format and content: HE sib.bed DMRs of  HE sibling compared with EC sibling and HSC sibling Supplementary files format and content: HSC sib.bed DMRs of  HSC sibling compared with EC sibling and HE sibling Supplementary files format and content: EC HE sib.bed DMRs of  EC and HE sibling Supplementary files format and content: HE HSC sib.bed DMRs of  HE and HSC sibling Supplementary files format and content: EC sib mut.bed DMRs of  EC sibling and EC mutant Supplementary files format and content: HE sib mut.bed DMRs of  HE sibling and HE mutant Supplementary files format and content: HSC sib mut.bed DMRs of  HSC sibling and HSC mutant", "endothelial cells", null, "Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3\u2032 biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification", null, "developmental stage:EC|genotype:dnmt1 mutant|region:AGM", "GSM5694245", "GSM5694245: EC mut rep2 RNA; Danio rerio; RNA Seq", "GSM5694245", null, "1", "Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3\u2032 biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification", "GEO Accession:GSM5694245", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP346708", null, null, "EC_sib_2_1_RNA.fq.gz EC_sib_2_2_RNA.fq.gz", "fastq fastq", 3166511400.0, 10555038.0, "GSM5694245 r1", "0:150 1:150", "A:953416270;C:589683319;G:624608777;T:998770674;N:32360", 150, 150, null, null, 953416270, 589683319, 624608777, 998770674, 32360, "SRX13164735", "SRS11095938", "SRA1331007", "GEO", "Institute of Hematology and Blood Diseases Hospital", 2, 0.90602, 0.89266, 0.283, 0.28004, 0.78804, 0.79259, 0.46429, 0.58332, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "strtseq", null, "China", "2021-11-18", "Undetermined", "Embryo", "Endothelium", "Cardiovascular System"], [67030, "SRR16973870", "SRX13164734", "SRS11095937", "SRP346708", "PRJNA781453", "WGBS and RNA seq of Danio rerio in HSPC generation", "GSE189072", "Other", "In this study  we interrogated the role of DNA methylation in HSPC generation by taking advantage of dnmt1 knockout/knockdown embryos in zebrafish. First  we generated a comprehensive DNA methylation landscape of EHT  which revealed gradually hypermethylated regions associated with vasculogenesis. Taking advantage of dnmt1 deficient embryos  we showed that the decreased DNA methylation blocked HSPC emergence. Mechanistically  we demonstrated that the decreased DNA methylation increased the expression of arterial genes and Notch signaling  thus contributing to defects in the EHT in dnmt1 deficient embryos. Herein  we identified that DNA methylation  as epigenetic regulator  participates in the negative modulation of Notch signaling through inhibiting transcription during HSPC generation in zebrafish. Overall design: WGBS and RNA seq of Danio rerio in EC HE and HSPC.", null, "pubmed:35502759", null, "EC mut rep1 RNA", "GSM5694244", null, "tissue:endothelial cells|developmental stage:EC|genotype:dnmt1 mutant|region:AGM", "EC mut rep1 RNA", "Basecalls perfomed using CASAVA2.19 WGBS and RNA seq raw sequencing reads were first trimmed for adapter and low quality sequences. Then mapped to GRCz11 using BS Seeker2v2.1.8 and hisat2v2.2.1 with parameters \" t Y  m 0.04   bt2  end to end\" and \"  known splicesite infile  p 30  k 10   dta  t\" separately. Student's T test was used to perform DMR analysis for WGBS data. Gene expression level was quantified by HTSeqv0.12.4 and differentially expressed genesDEGs were determined by DESeq2v1.30.1 Genome build: GRCz11 Supplementary files format and content: RNA seq raw count matrix Supplementary files format and content: raw count.txt raw counts Supplementary files format and content: EC sib.bed DMRs of  EC sibling compared with HE sibling and HSC sibling Supplementary files format and content: HE sib.bed DMRs of  HE sibling compared with EC sibling and HSC sibling Supplementary files format and content: HSC sib.bed DMRs of  HSC sibling compared with EC sibling and HE sibling Supplementary files format and content: EC HE sib.bed DMRs of  EC and HE sibling Supplementary files format and content: HE HSC sib.bed DMRs of  HE and HSC sibling Supplementary files format and content: EC sib mut.bed DMRs of  EC sibling and EC mutant Supplementary files format and content: HE sib mut.bed DMRs of  HE sibling and HE mutant Supplementary files format and content: HSC sib mut.bed DMRs of  HSC sibling and HSC mutant", "endothelial cells", null, "Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3\u2032 biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification", null, "developmental stage:EC|genotype:dnmt1 mutant|region:AGM", "GSM5694244", "GSM5694244: EC mut rep1 RNA; Danio rerio; RNA Seq", "GSM5694244", null, "1", "Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3\u2032 biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification", "GEO Accession:GSM5694244", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP346708", null, null, "EC_sib_1_1_RNA.fq.gz EC_sib_1_2_RNA.fq.gz", "fastq fastq", 3962208600.0, 13207362.0, "GSM5694244 r1", "0:150 1:150", "A:1157734424;C:769637879;G:815215301;T:1219572479;N:48517", 150, 150, null, null, 1157734424, 769637879, 815215301, 1219572479, 48517, "SRX13164734", "SRS11095937", "SRA1331007", "GEO", "Institute of Hematology and Blood Diseases Hospital", 2, 0.9138, 0.90509, 0.21931, 0.21725, 0.77479, 0.77741, 0.5314, 0.53073, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "strtseq", null, "China", "2021-11-18", "Undetermined", "Embryo", "Endothelium", "Cardiovascular System"], [67031, "SRR16973869", "SRX13164733", "SRS11095936", "SRP346708", "PRJNA781453", "WGBS and RNA seq of Danio rerio in HSPC generation", "GSE189072", "Other", "In this study  we interrogated the role of DNA methylation in HSPC generation by taking advantage of dnmt1 knockout/knockdown embryos in zebrafish. First  we generated a comprehensive DNA methylation landscape of EHT  which revealed gradually hypermethylated regions associated with vasculogenesis. Taking advantage of dnmt1 deficient embryos  we showed that the decreased DNA methylation blocked HSPC emergence. Mechanistically  we demonstrated that the decreased DNA methylation increased the expression of arterial genes and Notch signaling  thus contributing to defects in the EHT in dnmt1 deficient embryos. Herein  we identified that DNA methylation  as epigenetic regulator  participates in the negative modulation of Notch signaling through inhibiting transcription during HSPC generation in zebrafish. Overall design: WGBS and RNA seq of Danio rerio in EC HE and HSPC.", null, "pubmed:35502759", null, "EC sib rep3 RNA", "GSM5694243", null, "tissue:endothelial cells|developmental stage:EC|genotype:sibling|region:AGM", "EC sib rep3 RNA", "Basecalls perfomed using CASAVA2.19 WGBS and RNA seq raw sequencing reads were first trimmed for adapter and low quality sequences. Then mapped to GRCz11 using BS Seeker2v2.1.8 and hisat2v2.2.1 with parameters \" t Y  m 0.04   bt2  end to end\" and \"  known splicesite infile  p 30  k 10   dta  t\" separately. Student's T test was used to perform DMR analysis for WGBS data. Gene expression level was quantified by HTSeqv0.12.4 and differentially expressed genesDEGs were determined by DESeq2v1.30.1 Genome build: GRCz11 Supplementary files format and content: RNA seq raw count matrix Supplementary files format and content: raw count.txt raw counts Supplementary files format and content: EC sib.bed DMRs of  EC sibling compared with HE sibling and HSC sibling Supplementary files format and content: HE sib.bed DMRs of  HE sibling compared with EC sibling and HSC sibling Supplementary files format and content: HSC sib.bed DMRs of  HSC sibling compared with EC sibling and HE sibling Supplementary files format and content: EC HE sib.bed DMRs of  EC and HE sibling Supplementary files format and content: HE HSC sib.bed DMRs of  HE and HSC sibling Supplementary files format and content: EC sib mut.bed DMRs of  EC sibling and EC mutant Supplementary files format and content: HE sib mut.bed DMRs of  HE sibling and HE mutant Supplementary files format and content: HSC sib mut.bed DMRs of  HSC sibling and HSC mutant", "endothelial cells", null, "Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3\u2032 biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification", null, "developmental stage:EC|genotype:sibling|region:AGM", "GSM5694243", "GSM5694243: EC sib rep3 RNA; Danio rerio; RNA Seq", "GSM5694243", null, "1", "Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3\u2032 biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification", "GEO Accession:GSM5694243", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP346708", null, "loader:fastq load.py", "EC_mut_3_1_RNA.fq.gz EC_mut_3_2_RNA.fq.gz", "fastq fastq", 5214231600.0, 17380772.0, "GSM5694243 r1", "0:150 1:150", "A:1518201912;C:1020669101;G:1094674332;T:1580669249;N:17006", 150, 150, null, null, 1518201912, 1020669101, 1094674332, 1580669249, 17006, "SRX13164733", "SRS11095936", "SRA1331007", "GEO", "Institute of Hematology and Blood Diseases Hospital", 2, 0.91916, 0.91501, 0.28949, 0.28875, 0.77536, 0.77749, 0.54408, 0.54439, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "strtseq", null, "China", "2021-11-18", "Undetermined", "Embryo", "Endothelium", "Cardiovascular System"], [67032, "SRR16973868", "SRX13164732", "SRS11095935", "SRP346708", "PRJNA781453", "WGBS and RNA seq of Danio rerio in HSPC generation", "GSE189072", "Other", "In this study  we interrogated the role of DNA methylation in HSPC generation by taking advantage of dnmt1 knockout/knockdown embryos in zebrafish. First  we generated a comprehensive DNA methylation landscape of EHT  which revealed gradually hypermethylated regions associated with vasculogenesis. Taking advantage of dnmt1 deficient embryos  we showed that the decreased DNA methylation blocked HSPC emergence. Mechanistically  we demonstrated that the decreased DNA methylation increased the expression of arterial genes and Notch signaling  thus contributing to defects in the EHT in dnmt1 deficient embryos. Herein  we identified that DNA methylation  as epigenetic regulator  participates in the negative modulation of Notch signaling through inhibiting transcription during HSPC generation in zebrafish. Overall design: WGBS and RNA seq of Danio rerio in EC HE and HSPC.", null, "pubmed:35502759", null, "EC sib rep2 RNA", "GSM5694242", null, "tissue:endothelial cells|developmental stage:EC|genotype:sibling|region:AGM", "EC sib rep2 RNA", "Basecalls perfomed using CASAVA2.19 WGBS and RNA seq raw sequencing reads were first trimmed for adapter and low quality sequences. Then mapped to GRCz11 using BS Seeker2v2.1.8 and hisat2v2.2.1 with parameters \" t Y  m 0.04   bt2  end to end\" and \"  known splicesite infile  p 30  k 10   dta  t\" separately. Student's T test was used to perform DMR analysis for WGBS data. Gene expression level was quantified by HTSeqv0.12.4 and differentially expressed genesDEGs were determined by DESeq2v1.30.1 Genome build: GRCz11 Supplementary files format and content: RNA seq raw count matrix Supplementary files format and content: raw count.txt raw counts Supplementary files format and content: EC sib.bed DMRs of  EC sibling compared with HE sibling and HSC sibling Supplementary files format and content: HE sib.bed DMRs of  HE sibling compared with EC sibling and HSC sibling Supplementary files format and content: HSC sib.bed DMRs of  HSC sibling compared with EC sibling and HE sibling Supplementary files format and content: EC HE sib.bed DMRs of  EC and HE sibling Supplementary files format and content: HE HSC sib.bed DMRs of  HE and HSC sibling Supplementary files format and content: EC sib mut.bed DMRs of  EC sibling and EC mutant Supplementary files format and content: HE sib mut.bed DMRs of  HE sibling and HE mutant Supplementary files format and content: HSC sib mut.bed DMRs of  HSC sibling and HSC mutant", "endothelial cells", null, "Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3\u2032 biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification", null, "developmental stage:EC|genotype:sibling|region:AGM", "GSM5694242", "GSM5694242: EC sib rep2 RNA; Danio rerio; RNA Seq", "GSM5694242", null, "1", "Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3\u2032 biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification", "GEO Accession:GSM5694242", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP346708", null, null, "EC_mut_2_1_RNA.fq.gz EC_mut_2_2_RNA.fq.gz", "fastq fastq", 3551728200.0, 11839094.0, "GSM5694242 r1", "0:150 1:150", "A:1033665824;C:697141333;G:748608593;T:1072309959;N:2491", 150, 150, null, null, 1033665824, 697141333, 748608593, 1072309959, 2491, "SRX13164732", "SRS11095935", "SRA1331007", "GEO", "Institute of Hematology and Blood Diseases Hospital", 2, 0.91086, 0.91055, 0.22761, 0.22617, 0.76611, 0.77388, 0.54742, 0.54539, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "strtseq", null, "China", "2021-11-18", "Undetermined", "Embryo", "Endothelium", "Cardiovascular System"], [67033, "SRR16973867", "SRX13164731", "SRS11095934", "SRP346708", "PRJNA781453", "WGBS and RNA seq of Danio rerio in HSPC generation", "GSE189072", "Other", "In this study  we interrogated the role of DNA methylation in HSPC generation by taking advantage of dnmt1 knockout/knockdown embryos in zebrafish. First  we generated a comprehensive DNA methylation landscape of EHT  which revealed gradually hypermethylated regions associated with vasculogenesis. Taking advantage of dnmt1 deficient embryos  we showed that the decreased DNA methylation blocked HSPC emergence. Mechanistically  we demonstrated that the decreased DNA methylation increased the expression of arterial genes and Notch signaling  thus contributing to defects in the EHT in dnmt1 deficient embryos. Herein  we identified that DNA methylation  as epigenetic regulator  participates in the negative modulation of Notch signaling through inhibiting transcription during HSPC generation in zebrafish. Overall design: WGBS and RNA seq of Danio rerio in EC HE and HSPC.", null, "pubmed:35502759", null, "EC sib rep1 RNA", "GSM5694241", null, "tissue:endothelial cells|developmental stage:EC|genotype:sibling|region:AGM", "EC sib rep1 RNA", "Basecalls perfomed using CASAVA2.19 WGBS and RNA seq raw sequencing reads were first trimmed for adapter and low quality sequences. Then mapped to GRCz11 using BS Seeker2v2.1.8 and hisat2v2.2.1 with parameters \" t Y  m 0.04   bt2  end to end\" and \"  known splicesite infile  p 30  k 10   dta  t\" separately. Student's T test was used to perform DMR analysis for WGBS data. Gene expression level was quantified by HTSeqv0.12.4 and differentially expressed genesDEGs were determined by DESeq2v1.30.1 Genome build: GRCz11 Supplementary files format and content: RNA seq raw count matrix Supplementary files format and content: raw count.txt raw counts Supplementary files format and content: EC sib.bed DMRs of  EC sibling compared with HE sibling and HSC sibling Supplementary files format and content: HE sib.bed DMRs of  HE sibling compared with EC sibling and HSC sibling Supplementary files format and content: HSC sib.bed DMRs of  HSC sibling compared with EC sibling and HE sibling Supplementary files format and content: EC HE sib.bed DMRs of  EC and HE sibling Supplementary files format and content: HE HSC sib.bed DMRs of  HE and HSC sibling Supplementary files format and content: EC sib mut.bed DMRs of  EC sibling and EC mutant Supplementary files format and content: HE sib mut.bed DMRs of  HE sibling and HE mutant Supplementary files format and content: HSC sib mut.bed DMRs of  HSC sibling and HSC mutant", "endothelial cells", null, "Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3\u2032 biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification", null, "developmental stage:EC|genotype:sibling|region:AGM", "GSM5694241", "GSM5694241: EC sib rep1 RNA; Danio rerio; RNA Seq", "GSM5694241", null, "1", "Zebrafish embryos were harvested and dissected for single cell suspension. Single cell was sorted in lysis buffer by fluorescence activated cell sorting. The RNA seq library preparation and sequencing were performed based on the 3\u2032 biased single cell tagged reverse transcription sequencing STRT seq.The DNA libraries conduction were performed according to the scBS seq with some modification", "GEO Accession:GSM5694241", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP346708", null, null, "EC_mut_1_1_RNA.fq.gz EC_mut_1_2_RNA.fq.gz", "fastq fastq", 4174024500.0, 13913415.0, "GSM5694241 r1", "0:150 1:150", "A:1198561312;C:807832743;G:886085495;T:1281504164;N:40786", 150, 150, null, null, 1198561312, 807832743, 886085495, 1281504164, 40786, "SRX13164731", "SRS11095934", "SRA1331007", "GEO", "Institute of Hematology and Blood Diseases Hospital", 2, 0.9162, 0.91249, 0.25639, 0.25487, 0.7767, 0.78186, 0.45792, 0.43528, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "strtseq", null, "China", "2021-11-18", "Undetermined", "Embryo", "Endothelium", "Cardiovascular System"]], "truncated": false, "filtered_table_rows_count": 33, "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", 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false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation=Endothelium", "results": [{"value": "Embryo", "label": "Embryo", "count": 33, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation=Endothelium&devstage_curation_coarse=Embryo", "selected": false}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation=Endothelium", "results": [{"value": "Undetermined", "label": "Undetermined", "count": 33, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?tissue_curation=Endothelium", "selected": true}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Undetermined&tissue_curation=Endothelium", 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