{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation_coarse = \"Embryo\" and tissue_curation = \"Endothelium\"", "rows": [[38364, "SRR1793802", "SRX869237", "SRS840014", "SRP053359", "PRJNA274951", "Lymphatic vessels arise from a niche of multipotent angioblasts within the floor of the cardinal vein", "GSE65751", "Transcriptome Analysis", "How cells acquire their fate is a fundamental question in both developmental and regenerative biology. Multipotent progenitors undergo gradual cell fate restriction in response to temporal and positional cues from the microenvironment the nature of which is far from being clear. In the case of the lymphatic system venous endothelial cells are thought to give rise to lymphatic vessels through a process of trans differentiation. Upon expression of a set of transcription factors venous cells acquire a lymphatic fate and bud out to generate the lymphatic vasculature. In this work we challenge this view and show that while lymphatic endothelial cells LECs do arise in the Cardinal Vein CV they do so from a previously uncharacterized pool of multipotent angioblasts. Using lymphatic specific transgenic zebrafish in combination with endothelial photoconvertible reporters and long term live imaging we demonstrate that these multipotent angioblasts can generate not only lymphatic but also arterious and venous fates. We further reveal that the underlying endoderm serves as a source of Wnt5b which acts as a lymphatic inductive signal promoting the angioblast to lymphatic transition. Moreover Wnt5b induced lymphatic specification in human embryonic stem cells derived vascular progenitors suggesting that this process is evolutionary conserved. Our results uncover a novel mechanism of lymphatic vessel formation whereby multipotent angioblasts and not venous endothelial cells give rise to the lymphatic endothelium and provide the first characterization of their inductive niche. More broadly our findings highlight the CV as a plastic and heterogeneous structure containing different cell populations analogous to the hematopoietic niche in the aortic floor. Overall design: Following Kaede photoconversion of dorsal or ventral halves of the PCV in Tgfli1:gal4;uasKaede embryos at 24 hpf 6\u00a0embryos per group were used for FACS isolation of Kaede photconverted red ECs.", null, "pubmed:25992545", null, "d red ZF sample 0012", "GSM1604058", null, "tissue:Dorsal endothelial cells|strain:Tgfli1:gal4; uasKaede|developmental stage:24hpf", "d red ZF sample 0012", "Libraries were sequenced on the Illumina HiSeq2500 according to standard paired end sequencing protocols. 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We further reveal that the underlying endoderm serves as a source of Wnt5b which acts as a lymphatic inductive signal promoting the angioblast to lymphatic transition. Moreover Wnt5b induced lymphatic specification in human embryonic stem cells derived vascular progenitors suggesting that this process is evolutionary conserved. Our results uncover a novel mechanism of lymphatic vessel formation whereby multipotent angioblasts and not venous endothelial cells give rise to the lymphatic endothelium and provide the first characterization of their inductive niche. More broadly our findings highlight the CV as a plastic and heterogeneous structure containing different cell populations analogous to the hematopoietic niche in the aortic floor. Overall design: Following Kaede photoconversion of dorsal or ventral halves of the PCV in Tgfli1:gal4;uasKaede embryos at 24 hpf 6\u00a0embryos per group were used for FACS isolation of Kaede photconverted red ECs.", null, "pubmed:25992545", null, "d red ZF sample 0008", "GSM1604057", null, "tissue:Dorsal endothelial cells|strain:Tgfli1:gal4; uasKaede|developmental stage:24hpf", "d red ZF sample 0008", "Libraries were sequenced on the Illumina HiSeq2500 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 20. trimming of read2 to 35 bases not required. 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We further reveal that the underlying endoderm serves as a source of Wnt5b which acts as a lymphatic inductive signal promoting the angioblast to lymphatic transition. Moreover Wnt5b induced lymphatic specification in human embryonic stem cells derived vascular progenitors suggesting that this process is evolutionary conserved. Our results uncover a novel mechanism of lymphatic vessel formation whereby multipotent angioblasts and not venous endothelial cells give rise to the lymphatic endothelium and provide the first characterization of their inductive niche. More broadly our findings highlight the CV as a plastic and heterogeneous structure containing different cell populations analogous to the hematopoietic niche in the aortic floor. Overall design: Following Kaede photoconversion of dorsal or ventral halves of the PCV in Tgfli1:gal4;uasKaede embryos at 24 hpf 6\u00a0embryos per group were used for FACS isolation of Kaede photconverted red ECs.", null, "pubmed:25992545", null, "V red ZF sample 0011", "GSM1604056", null, "tissue:Ventral endothelial cells|strain:Tgfli1:gal4; uasKaede|developmental stage:24hpf", "V red ZF sample 0011", "Libraries were sequenced on the Illumina HiSeq2500 according to standard paired end sequencing protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl fastq cluster count 1234567890 mismatches 0 use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 20. trimming of read2 to 35 bases not required. 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We further reveal that the underlying endoderm serves as a source of Wnt5b which acts as a lymphatic inductive signal promoting the angioblast to lymphatic transition. Moreover Wnt5b induced lymphatic specification in human embryonic stem cells derived vascular progenitors suggesting that this process is evolutionary conserved. Our results uncover a novel mechanism of lymphatic vessel formation whereby multipotent angioblasts and not venous endothelial cells give rise to the lymphatic endothelium and provide the first characterization of their inductive niche. More broadly our findings highlight the CV as a plastic and heterogeneous structure containing different cell populations analogous to the hematopoietic niche in the aortic floor. 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CEL Seq Hashimshony et al. 2012 demultiplexing of second mate using first mate barcode allowing no mismatches in barcode. bowtie2 version 2.1.0 against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations. Reads with the same unique molecular identifiers UMIs were colapsed for transcript counting. Genome build: Zv9 Supplementary files format and content: Tabular expression matrix includes number of transcript molecules.", "Ventral endothelial cells", null, "RNA was isolated using TRIzol with addition of ERCC spike ins and GenElute LPA Sigma The CEL Seq protocol Hashimshony et al. 2012 was used to amplify and sequence. CEL Seq multiplexing barocdes with slite modification were used. 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Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate", "parent bioproject:PRJNA321317", "pubmed:28350988;pubmed:33273096", null, "NoEndo 48hpf E2", "GSM2150816", null, "source name:Endothelial cell|developmental stage:48hpf|tissue:Endothelial|stain:GFP", "NoEndo 48hpf E2", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...", "Endothelial cell", null, "Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. 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Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM2150816", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer", null, "SRP074848", null, null, "NoEndo_48hpf_E2.fastq.gz", "fastq", 553364740.0, 7281115.0, "GSM2150816 r1", "0:76", "A:129173344;C:134804122;G:141026546;T:148331467;N:29261", 76, null, null, null, 129173344, 134804122, 141026546, 148331467, 29261, "SRX1756837", "SRS1433368", "SRA424808", "GEO", "Internal Medicine, Yale University", 1, 1e-05, null, 0.0, null, 0.99997, null, 0.0, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-05-11", "Hatching", "Embryo", "Endothelium", "Cardiovascular System"], [40976, "SRR3498290", "SRX1756836", "SRS1433367", "SRP074848", "PRJNA321321", "microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues", "GSE81340", "Transcriptome Analysis", "Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate", "parent bioproject:PRJNA321317", "pubmed:28350988;pubmed:33273096", null, "NoEndo 48hpf E1", "GSM2150815", null, "source name:Endothelial cell|developmental stage:48hpf|tissue:Endothelial|stain:GFP", "NoEndo 48hpf E1", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...", "Endothelial cell", null, "Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols", "Zebrafish embryos were raised according standard protocols at 28\u02daC and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.", "developmental stage:48hpf|tissue:Endothelial|stain:GFP", "GSM2150815", "GSM2150815: NoEndo 48hpf E1; Danio rerio; miRNA Seq", "GSM2150815", null, "1", "Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM2150815", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer", null, "SRP074848", null, null, "NoEndo_48hpf_E1.fastq.gz", "fastq", 1204752152.0, 15852002.0, "GSM2150815 r1", "0:76", "A:297517299;C:293969730;G:317491224;T:295696492;N:77407", 76, null, null, null, 297517299, 293969730, 317491224, 295696492, 77407, "SRX1756836", "SRS1433367", "SRA424808", "GEO", "Internal Medicine, Yale University", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-05-11", "Hatching", "Embryo", "Endothelium", "Cardiovascular System"], [40977, "SRR3498289", "SRX1756835", "SRS1433366", "SRP074848", "PRJNA321321", "microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues", "GSE81340", "Transcriptome Analysis", "Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate", "parent bioproject:PRJNA321317", "pubmed:28350988;pubmed:33273096", null, "NoEndo 24hpf E1", "GSM2150814", null, "source name:Endothelial cell|developmental stage:24hpf|tissue:Endothelial|stain:GFP", "NoEndo 24hpf E1", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...", "Endothelial cell", null, "Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols", "Zebrafish embryos were raised according standard protocols at 28\u02daC and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.", "developmental stage:24hpf|tissue:Endothelial|stain:GFP", "GSM2150814", "GSM2150814: NoEndo 24hpf E1; Danio rerio; miRNA Seq", "GSM2150814", null, "1", "Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM2150814", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer", null, "SRP074848", null, null, "NoEndo_24hpf_E1.fastq.gz", "fastq", 1422085704.0, 18711654.0, "GSM2150814 r1", "0:76", "A:347700492;C:356065333;G:376424133;T:341806001;N:89745", 76, null, null, null, 347700492, 356065333, 376424133, 341806001, 89745, "SRX1756835", "SRS1433366", "SRA424808", "GEO", "Internal Medicine, Yale University", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-05-11", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [40981, "SRR3498285", "SRX1756831", "SRS1433362", "SRP074848", "PRJNA321321", "microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues", "GSE81340", "Transcriptome Analysis", "Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate", "parent bioproject:PRJNA321317", "pubmed:28350988;pubmed:33273096", null, "Endo 48hpf E2", "GSM2150810", null, "source name:Endothelial cell|developmental stage:48hpf|tissue:Endothelial|stain:GFP", "Endo 48hpf E2", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...", "Endothelial cell", null, "Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols", "Zebrafish embryos were raised according standard protocols at 28\u02daC and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.", "developmental stage:48hpf|tissue:Endothelial|stain:GFP", "GSM2150810", "GSM2150810: Endo 48hpf E2; Danio rerio; miRNA Seq", "GSM2150810", null, "1", "Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM2150810", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer", null, "SRP074848", null, null, "Endo_48hpf_E2.fastq.gz", "fastq", 1254556624.0, 16507324.0, "GSM2150810 r1", "0:76", "A:316229540;C:323340793;G:307552357;T:307354555;N:79379", 76, null, null, null, 316229540, 323340793, 307552357, 307354555, 79379, "SRX1756831", "SRS1433362", "SRA424808", "GEO", "Internal Medicine, Yale University", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-05-11", "Hatching", "Embryo", "Endothelium", "Cardiovascular System"], [40982, "SRR3498284", "SRX1756830", "SRS1433361", "SRP074848", "PRJNA321321", "microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues", "GSE81340", "Transcriptome Analysis", "Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate", "parent bioproject:PRJNA321317", "pubmed:28350988;pubmed:33273096", null, "Endo 48hpf E1", "GSM2150809", null, "source name:Endothelial cell|developmental stage:48hpf|tissue:Endothelial|stain:GFP", "Endo 48hpf E1", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...", "Endothelial cell", null, "Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols", "Zebrafish embryos were raised according standard protocols at 28\u02daC and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.", "developmental stage:48hpf|tissue:Endothelial|stain:GFP", "GSM2150809", "GSM2150809: Endo 48hpf E1; Danio rerio; miRNA Seq", "GSM2150809", null, "1", "Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM2150809", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer", null, "SRP074848", null, null, "Endo_48hpf_E1.fastq.gz", "fastq", 1449497080.0, 19072330.0, "GSM2150809 r1", "0:76", "A:362564557;C:370330864;G:364749441;T:351760774;N:91444", 76, null, null, null, 362564557, 370330864, 364749441, 351760774, 91444, "SRX1756830", "SRS1433361", "SRA424808", "GEO", "Internal Medicine, Yale University", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-05-11", "Hatching", "Embryo", "Endothelium", "Cardiovascular System"], [40983, "SRR3498283", "SRX1756829", "SRS1433360", "SRP074848", "PRJNA321321", "microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues", "GSE81340", "Transcriptome Analysis", "Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate", "parent bioproject:PRJNA321317", "pubmed:28350988;pubmed:33273096", null, "Endo 24hpf E1", "GSM2150808", null, "source name:Endothelial cell|developmental stage:24hpf|tissue:Endothelial|stain:GFP", "Endo 24hpf E1", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...", "Endothelial cell", null, "Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols", "Zebrafish embryos were raised according standard protocols at 28\u02daC and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.", "developmental stage:24hpf|tissue:Endothelial|stain:GFP", "GSM2150808", "GSM2150808: Endo 24hpf E1; Danio rerio; miRNA Seq", "GSM2150808", null, "1", "Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM2150808", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer", null, "SRP074848", null, null, "Endo_24hpf_E1.fastq.gz", "fastq", 1527500440.0, 20098690.0, "GSM2150808 r1", "0:76", "A:356712587;C:354608109;G:432977038;T:383106520;N:96186", 76, null, null, null, 356712587, 354608109, 432977038, 383106520, 96186, "SRX1756829", "SRS1433360", "SRA424808", "GEO", "Internal Medicine, Yale University", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-05-11", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [41146, "SRR3742564", "SRX1896783", "SRS1539775", "SRP077871", "PRJNA327749", "Gene expression profiles of endothelial cells from mutants and siblings of tsu3994", "GSE83987", "Transcriptome Analysis", "Through RNA seq we report endothelial cells from mutants had 1063 up regulated and 132 down regulated genes >2.0 fold with false discovery rate <0.001 when compared to siblings. Overall design: Examination of gene exprssion profiles of endothelial cells from siblings and mutants of tsu3994", null, "pubmed:28003365", null, "Mt", "GSM2224910", null, "tissue:kdrl:GFP+ Endothelial cells|genetic background:tsu3994;Tgkdrl;GFP cross|genotype/variation:Morphologically mutant embryo|Stage:44 hpf type:Endothelial cells", "Mt", "HCS3.3.20 RTA 2.5.2 and bcl2fastq2 v2.16 were used for basecalling. Sequenced reads were remove reads with adaptors and remove reads in which unknown bases are more than 10% remove reads in which unknown bases are more than 10%.We use Bowtie2 with parameters q phred64 sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 to map clean reads to reference gene and use BWA with parameters o 1 e 50 i 50 L k 2 l 31 t 4 q 10 to reference genome Danio rerio.GRCz10.dna.toplevel.fa . RSEM is a quantification tool that computed Maximum likelihood abundance estimates using the Expectation Maximization EM algorithm for its statistical model . FPKM fragment Per Kilobase of gene per Megabase of library size method is used in calculated expression level. Genome build: Zv10 Supplementary files format and content: tab delimited text files include FPKM values for each Sample", "kdrl:GFP+ Endothelial cells", null, "Morphologically normal siblings and mutant embryos from crosses of Tgkdrl:GFP; gbf1tsu3994/+ at 44 hpf were dechorionated and disintegrated completely to prepare single cell suspension. Then kdrl:GFP+ ECs were sorted by flow cytomer FACSAria BD and MoFlo XDP BeckMan and positive cells were confirmed by microscopy. Total mRNAs were extracted with RNeasy Mini Kit QIAGEN. The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo dT magnetic beads. Mixed with the fragmentation buffer the mRNA is fragmented into short fragments. Then the first strand of cDNA is synthesized by using random hexamer primer. Buffer dNTPs RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3\u2019 end single nucleotide A adenine addition is then performed. Finally sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification.During the QC step Agilent 2100 Bioanaylzer and ABI StepOnePlus Real Time PCR System are used to qualify and quantify of the sample library. The library products are ready for sequencing via Illumina HiSeqTM 2000 or other sequencer when necessary.", null, "genetic background:tsu3994;Tgkdrl;GFP cross|genotype/variation:Morphologically mutant embryo|Stage:44 hpf type:Endothelial cells", "GSM2224910", "GSM2224910: Mt; Danio rerio; RNA Seq", "GSM2224910", null, "1", "Morphologically normal siblings and mutant embryos from crosses of Tgkdrl:GFP; gbf1tsu3994/+ at 44 hpf were dechorionated and disintegrated completely to prepare single cell suspension. Then kdrl:GFP+ ECs were sorted by flow cytomer FACSAria BD and MoFlo XDP BeckMan and positive cells were confirmed by microscopy. Total mRNAs were extracted with RNeasy Mini Kit QIAGEN. The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo dT magnetic beads. Mixed with the fragmentation buffer the mRNA is fragmented into short fragments. Then the first strand of cDNA is synthesized by using random hexamer primer. Buffer dNTPs RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3\u2019 end single nucleotide A adenine addition is then performed. Finally sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification.During the QC step Agilent 2100 Bioanaylzer and ABI StepOnePlus Real Time PCR System are used to qualify and quantify of the sample library. The library products are ready for sequencing via Illumina HiSeqTM 2000 or other sequencer when necessary.", "GEO Accession:GSM2224910", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP077871", null, null, "160123_I114_FCH52M2BBXX_L2_WHFISoiqRAABRAAPEI-144_1.fq.gz", "fastq", 262444686.0, 5356014.0, "GSM2224910 r1", "0:49", "A:66548564;C:63544339;G:66582385;T:65755749;N:13649", 49, null, null, null, 66548564, 63544339, 66582385, 65755749, 13649, "SRX1896783", "SRS1539775", "SRA437681", "GEO", "Anming Meng, School of Lifesciences, Tsinghua University", 1, 0.92714, null, 0.05568, null, 0.73423, null, 0.48371, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2016-07-04", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [41147, "SRR3742565", "SRX1896783", "SRS1539775", "SRP077871", "PRJNA327749", "Gene expression profiles of endothelial cells from mutants and siblings of tsu3994", "GSE83987", "Transcriptome Analysis", "Through RNA seq we report endothelial cells from mutants had 1063 up regulated and 132 down regulated genes >2.0 fold with false discovery rate <0.001 when compared to siblings. Overall design: Examination of gene exprssion profiles of endothelial cells from siblings and mutants of tsu3994", null, "pubmed:28003365", null, "Mt", "GSM2224910", null, "tissue:kdrl:GFP+ Endothelial cells|genetic background:tsu3994;Tgkdrl;GFP cross|genotype/variation:Morphologically mutant embryo|Stage:44 hpf type:Endothelial cells", "Mt", "HCS3.3.20 RTA 2.5.2 and bcl2fastq2 v2.16 were used for basecalling. Sequenced reads were remove reads with adaptors and remove reads in which unknown bases are more than 10% remove reads in which unknown bases are more than 10%.We use Bowtie2 with parameters q phred64 sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 to map clean reads to reference gene and use BWA with parameters o 1 e 50 i 50 L k 2 l 31 t 4 q 10 to reference genome Danio rerio.GRCz10.dna.toplevel.fa . RSEM is a quantification tool that computed Maximum likelihood abundance estimates using the Expectation Maximization EM algorithm for its statistical model . FPKM fragment Per Kilobase of gene per Megabase of library size method is used in calculated expression level. Genome build: Zv10 Supplementary files format and content: tab delimited text files include FPKM values for each Sample", "kdrl:GFP+ Endothelial cells", null, "Morphologically normal siblings and mutant embryos from crosses of Tgkdrl:GFP; gbf1tsu3994/+ at 44 hpf were dechorionated and disintegrated completely to prepare single cell suspension. Then kdrl:GFP+ ECs were sorted by flow cytomer FACSAria BD and MoFlo XDP BeckMan and positive cells were confirmed by microscopy. Total mRNAs were extracted with RNeasy Mini Kit QIAGEN. The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo dT magnetic beads. Mixed with the fragmentation buffer the mRNA is fragmented into short fragments. Then the first strand of cDNA is synthesized by using random hexamer primer. Buffer dNTPs RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3\u2019 end single nucleotide A adenine addition is then performed. Finally sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification.During the QC step Agilent 2100 Bioanaylzer and ABI StepOnePlus Real Time PCR System are used to qualify and quantify of the sample library. The library products are ready for sequencing via Illumina HiSeqTM 2000 or other sequencer when necessary.", null, "genetic background:tsu3994;Tgkdrl;GFP cross|genotype/variation:Morphologically mutant embryo|Stage:44 hpf type:Endothelial cells", "GSM2224910", "GSM2224910: Mt; Danio rerio; RNA Seq", "GSM2224910", null, "1", "Morphologically normal siblings and mutant embryos from crosses of Tgkdrl:GFP; gbf1tsu3994/+ at 44 hpf were dechorionated and disintegrated completely to prepare single cell suspension. Then kdrl:GFP+ ECs were sorted by flow cytomer FACSAria BD and MoFlo XDP BeckMan and positive cells were confirmed by microscopy. Total mRNAs were extracted with RNeasy Mini Kit QIAGEN. The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo dT magnetic beads. Mixed with the fragmentation buffer the mRNA is fragmented into short fragments. Then the first strand of cDNA is synthesized by using random hexamer primer. Buffer dNTPs RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3\u2019 end single nucleotide A adenine addition is then performed. Finally sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification.During the QC step Agilent 2100 Bioanaylzer and ABI StepOnePlus Real Time PCR System are used to qualify and quantify of the sample library. The library products are ready for sequencing via Illumina HiSeqTM 2000 or other sequencer when necessary.", "GEO Accession:GSM2224910", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP077871", null, null, "160204_I136_FCH55MNBBXX_L6_WHFISoiqRAABRAAPEI-144_1.fq.gz", "fastq", 448147973.0, 9145877.0, "GSM2224910 r2", "0:49", "A:113623842;C:108767789;G:113689061;T:112055179;N:12102", 49, null, null, null, 113623842, 108767789, 113689061, 112055179, 12102, "SRX1896783", "SRS1539775", "SRA437681", "GEO", "Anming Meng, School of Lifesciences, Tsinghua University", 1, 0.91636, null, 0.05377, null, 0.73545, null, 0.48441, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2016-07-04", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [41148, "SRR3742562", "SRX1896782", "SRS1539774", "SRP077871", "PRJNA327749", "Gene expression profiles of endothelial cells from mutants and siblings of tsu3994", "GSE83987", "Transcriptome Analysis", "Through RNA seq we report endothelial cells from mutants had 1063 up regulated and 132 down regulated genes >2.0 fold with false discovery rate <0.001 when compared to siblings. Overall design: Examination of gene exprssion profiles of endothelial cells from siblings and mutants of tsu3994", null, "pubmed:28003365", null, "Sib", "GSM2224909", null, "tissue:kdrl:GFP+ Endothelial cells|genetic background:tsu3994;Tgkdrl;GFP cross|genotype/variation:Morphologically normal siblings embryo|Stage:44 hpf type:Endothelial cells", "Sib", "HCS3.3.20 RTA 2.5.2 and bcl2fastq2 v2.16 were used for basecalling. Sequenced reads were remove reads with adaptors and remove reads in which unknown bases are more than 10% remove reads in which unknown bases are more than 10%.We use Bowtie2 with parameters q phred64 sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 to map clean reads to reference gene and use BWA with parameters o 1 e 50 i 50 L k 2 l 31 t 4 q 10 to reference genome Danio rerio.GRCz10.dna.toplevel.fa . RSEM is a quantification tool that computed Maximum likelihood abundance estimates using the Expectation Maximization EM algorithm for its statistical model . FPKM fragment Per Kilobase of gene per Megabase of library size method is used in calculated expression level. Genome build: Zv10 Supplementary files format and content: tab delimited text files include FPKM values for each Sample", "kdrl:GFP+ Endothelial cells", null, "Morphologically normal siblings and mutant embryos from crosses of Tgkdrl:GFP; gbf1tsu3994/+ at 44 hpf were dechorionated and disintegrated completely to prepare single cell suspension. Then kdrl:GFP+ ECs were sorted by flow cytomer FACSAria BD and MoFlo XDP BeckMan and positive cells were confirmed by microscopy. Total mRNAs were extracted with RNeasy Mini Kit QIAGEN. The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo dT magnetic beads. Mixed with the fragmentation buffer the mRNA is fragmented into short fragments. Then the first strand of cDNA is synthesized by using random hexamer primer. Buffer dNTPs RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3\u2019 end single nucleotide A adenine addition is then performed. Finally sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification.During the QC step Agilent 2100 Bioanaylzer and ABI StepOnePlus Real Time PCR System are used to qualify and quantify of the sample library. The library products are ready for sequencing via Illumina HiSeqTM 2000 or other sequencer when necessary.", null, "genetic background:tsu3994;Tgkdrl;GFP cross|genotype/variation:Morphologically normal siblings embryo|Stage:44 hpf type:Endothelial cells", "GSM2224909", "GSM2224909: Sib; Danio rerio; RNA Seq", "GSM2224909", null, "1", "Morphologically normal siblings and mutant embryos from crosses of Tgkdrl:GFP; gbf1tsu3994/+ at 44 hpf were dechorionated and disintegrated completely to prepare single cell suspension. Then kdrl:GFP+ ECs were sorted by flow cytomer FACSAria BD and MoFlo XDP BeckMan and positive cells were confirmed by microscopy. Total mRNAs were extracted with RNeasy Mini Kit QIAGEN. The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo dT magnetic beads. Mixed with the fragmentation buffer the mRNA is fragmented into short fragments. Then the first strand of cDNA is synthesized by using random hexamer primer. Buffer dNTPs RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3\u2019 end single nucleotide A adenine addition is then performed. Finally sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification.During the QC step Agilent 2100 Bioanaylzer and ABI StepOnePlus Real Time PCR System are used to qualify and quantify of the sample library. The library products are ready for sequencing via Illumina HiSeqTM 2000 or other sequencer when necessary.", "GEO Accession:GSM2224909", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP077871", null, null, "160123_I114_FCH52M2BBXX_L2_WHFISoiqRAAARAAPEI-100_1.fq.gz", "fastq", 180708423.0, 3687927.0, "GSM2224909 r1", "0:49", "A:45675389;C:44261209;G:46002295;T:44768361;N:1169", 49, null, null, null, 45675389, 44261209, 46002295, 44768361, 1169, "SRX1896782", "SRS1539774", "SRA437681", "GEO", "Anming Meng, School of Lifesciences, Tsinghua University", 1, 0.93956, null, 0.0479, null, 0.75276, null, 0.47889, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2016-07-04", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [41149, "SRR3742563", "SRX1896782", "SRS1539774", "SRP077871", "PRJNA327749", "Gene expression profiles of endothelial cells from mutants and siblings of tsu3994", "GSE83987", "Transcriptome Analysis", "Through RNA seq we report endothelial cells from mutants had 1063 up regulated and 132 down regulated genes >2.0 fold with false discovery rate <0.001 when compared to siblings. Overall design: Examination of gene exprssion profiles of endothelial cells from siblings and mutants of tsu3994", null, "pubmed:28003365", null, "Sib", "GSM2224909", null, "tissue:kdrl:GFP+ Endothelial cells|genetic background:tsu3994;Tgkdrl;GFP cross|genotype/variation:Morphologically normal siblings embryo|Stage:44 hpf type:Endothelial cells", "Sib", "HCS3.3.20 RTA 2.5.2 and bcl2fastq2 v2.16 were used for basecalling. Sequenced reads were remove reads with adaptors and remove reads in which unknown bases are more than 10% remove reads in which unknown bases are more than 10%.We use Bowtie2 with parameters q phred64 sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 p 16 k 200 to map clean reads to reference gene and use BWA with parameters o 1 e 50 i 50 L k 2 l 31 t 4 q 10 to reference genome Danio rerio.GRCz10.dna.toplevel.fa . RSEM is a quantification tool that computed Maximum likelihood abundance estimates using the Expectation Maximization EM algorithm for its statistical model . FPKM fragment Per Kilobase of gene per Megabase of library size method is used in calculated expression level. Genome build: Zv10 Supplementary files format and content: tab delimited text files include FPKM values for each Sample", "kdrl:GFP+ Endothelial cells", null, "Morphologically normal siblings and mutant embryos from crosses of Tgkdrl:GFP; gbf1tsu3994/+ at 44 hpf were dechorionated and disintegrated completely to prepare single cell suspension. Then kdrl:GFP+ ECs were sorted by flow cytomer FACSAria BD and MoFlo XDP BeckMan and positive cells were confirmed by microscopy. Total mRNAs were extracted with RNeasy Mini Kit QIAGEN. The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo dT magnetic beads. Mixed with the fragmentation buffer the mRNA is fragmented into short fragments. Then the first strand of cDNA is synthesized by using random hexamer primer. Buffer dNTPs RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3\u2019 end single nucleotide A adenine addition is then performed. Finally sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification.During the QC step Agilent 2100 Bioanaylzer and ABI StepOnePlus Real Time PCR System are used to qualify and quantify of the sample library. The library products are ready for sequencing via Illumina HiSeqTM 2000 or other sequencer when necessary.", null, "genetic background:tsu3994;Tgkdrl;GFP cross|genotype/variation:Morphologically normal siblings embryo|Stage:44 hpf type:Endothelial cells", "GSM2224909", "GSM2224909: Sib; Danio rerio; RNA Seq", "GSM2224909", null, "1", "Morphologically normal siblings and mutant embryos from crosses of Tgkdrl:GFP; gbf1tsu3994/+ at 44 hpf were dechorionated and disintegrated completely to prepare single cell suspension. Then kdrl:GFP+ ECs were sorted by flow cytomer FACSAria BD and MoFlo XDP BeckMan and positive cells were confirmed by microscopy. Total mRNAs were extracted with RNeasy Mini Kit QIAGEN. The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo dT magnetic beads. Mixed with the fragmentation buffer the mRNA is fragmented into short fragments. Then the first strand of cDNA is synthesized by using random hexamer primer. Buffer dNTPs RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3\u2019 end single nucleotide A adenine addition is then performed. Finally sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification.During the QC step Agilent 2100 Bioanaylzer and ABI StepOnePlus Real Time PCR System are used to qualify and quantify of the sample library. The library products are ready for sequencing via Illumina HiSeqTM 2000 or other sequencer when necessary.", "GEO Accession:GSM2224909", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP077871", null, null, "160204_I136_FCH55MNBBXX_L6_WHFISoiqRAAARAAPEI-100_1.fq.gz", "fastq", 454459418.0, 9274682.0, "GSM2224909 r2", "0:49", "A:114982478;C:111450118;G:115561207;T:112452344;N:13271", 49, null, null, null, 114982478, 111450118, 115561207, 112452344, 13271, "SRX1896782", "SRS1539774", "SRA437681", "GEO", "Anming Meng, School of Lifesciences, Tsinghua University", 1, 0.92536, null, 0.04644, null, 0.75103, null, 0.47559, null, 49, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "China", "2016-07-04", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [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. 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", "GSM2432104", "GSM2432104: wt clutch1; Danio rerio; RNA Seq", "GSM2432104", 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: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. 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", "GSM2432102", "GSM2432102: kdrl:cxcr1 clutch1; Danio rerio; RNA Seq", "GSM2432102", 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: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. 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 B2", "nicoli mutmir AG01646", null, "strain:TU/AB|age:27.0|sex:pooled male and female|tissue:endothelial cells|molecule:mRNA|condition:miR 139|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "QuantSeq mutant miRNAs WT miR139 B2", "AG01646.1", "AG01646.1", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "unspecified", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP099466", null, null, "AG01646.1_R1.fastq.gz", "fastq", 1484740104.0, 19536054.0, "AG01646.1 R1.fastq.gz", "0:76", "A:453388316;C:246477203;G:365031959;T:419816346;N:26280", 76, null, null, null, 453388316, 246477203, 365031959, 419816346, 26280, "SRX2557170", "SRS1974563", "SRA537606", "Yale University|Genetics", "Yale University", 1, 0.82649, null, 0.1897, null, 0.79862, null, 0.52759, 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"], [41829, "SRR5251444", "SRX2557169", "SRS1974562", "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 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"], [42141, "SRR5443688", "SRX2733020", "SRS2120917", "SRP103805", "PRJNA382558", "mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.", "GSE97649", "Transcriptome Analysis", "48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. 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RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols", null, "transgene:kdrl eGFP|genotype:wildtype", "GSM2574368", "GSM2574368: 48hpf zebrafish FAC sorted endothelial cell wt 1; Danio rerio; RNA Seq", "GSM2574368", null, "1", "48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM2574368", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP103805", null, null, "S1_S1_L002_R1_001.fastq.gz", "fastq", 1073108602.0, 14221959.0, "GSM2574368 r2", "0:75.45 1:0", "A:261964537;C:270187564;G:253958473;T:286941827;N:56201", 75, 0, null, null, 261964537, 270187564, 253958473, 286941827, 56201, "SRX2733015", "SRS2120913", "SRA553927", "GEO", "Australian Institute for Bioengineering and Nanotechnology", 1, 0.93746, null, 0.05835, null, 0.73734, null, 0.50609, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2017-04-11", "Hatching", "Embryo", "Endothelium", "Cardiovascular System"], [42163, "SRR5443670", "SRX2733015", "SRS2120913", "SRP103805", "PRJNA382558", "mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.", "GSE97649", "Transcriptome Analysis", "48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate with 6 brains used per samples. Overall design: wild type vs mutant", null, "pubmed:26253536", null, "48hpf zebrafish FAC sorted endothelial cell wt 1", "GSM2574368", null, "tissue:purified endothelial cell|transgene:kdrl eGFP|genotype:wildtype", "48hpf zebrafish FAC sorted endothelial cell wt 1", "adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample", "purified endothelial cell", null, "48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols", null, "transgene:kdrl eGFP|genotype:wildtype", "GSM2574368", "GSM2574368: 48hpf zebrafish FAC sorted endothelial cell wt 1; Danio rerio; RNA Seq", "GSM2574368", null, "1", "48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM2574368", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP103805", null, null, "S1_S1_L003_R1_001.fastq.gz", "fastq", 1064653834.0, 14110138.0, "GSM2574368 r3", "0:75.45 1:0", "A:261657368;C:268193214;G:251551872;T:283215565;N:35815", 75, 0, null, null, 261657368, 268193214, 251551872, 283215565, 35815, "SRX2733015", "SRS2120913", "SRA553927", "GEO", "Australian Institute for Bioengineering and Nanotechnology", 1, 0.93651, null, 0.05738, null, 0.74042, null, 0.51489, null, 74, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2017-04-11", "Hatching", "Embryo", "Endothelium", "Cardiovascular System"], [42164, "SRR5443671", "SRX2733015", "SRS2120913", "SRP103805", "PRJNA382558", "mafba is a downstream transcriptional effector of Vegfc signaling essential for embryonic lymphangiogenesis in zebrafish.", "GSE97649", "Transcriptome Analysis", "48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate with 6 brains used per samples. Overall design: wild type vs mutant", null, "pubmed:26253536", null, "48hpf zebrafish FAC sorted endothelial cell wt 1", "GSM2574368", null, "tissue:purified endothelial cell|transgene:kdrl eGFP|genotype:wildtype", "48hpf zebrafish FAC sorted endothelial cell wt 1", "adaptor trimming done by bcl2fastq2 Reads were mapped against the reference genome danRer7/Zv9 using STAR Dobin et al. 2013 and read counts for each gene in the Ensembl annotation were generated using htseq count in the HTSeq python package Anders et al. 2015. Genome build: danRer7/Zv9 Supplementary files format and content: Tab delimited text files include yugene normalised data for each sample", "purified endothelial cell", null, "48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols", null, "transgene:kdrl eGFP|genotype:wildtype", "GSM2574368", "GSM2574368: 48hpf zebrafish FAC sorted endothelial cell wt 1; Danio rerio; RNA Seq", "GSM2574368", null, "1", "48hpf kdrl:egfp zebrafish brains were dissociated using Liberase and pdgfr beta egfp postive cells FAC sorted into Trizol LS. RNA was extracted and amplified before sequencing. Samples were prepared in triplicate. libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM2574368", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP103805", null, null, "S1_S1_L004_R1_001.fastq.gz", "fastq", 1072543375.0, 14214599.0, "GSM2574368 r4", "0:75.45 1:0", "A:263268340;C:270054371;G:253632532;T:285551360;N:36772", 75, 0, null, null, 263268340, 270054371, 253632532, 285551360, 36772, "SRX2733015", "SRS2120913", "SRA553927", "GEO", "Australian Institute for Bioengineering and Nanotechnology", 1, 0.93658, null, 0.05706, null, 0.73935, null, 0.5115, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2017-04-11", "Hatching", "Embryo", "Endothelium", "Cardiovascular System"], [47740, "SRR6848349", "SRX3803619", "SRS3055252", "SRP135898", "PRJNA438687", "Transcriptome profiling of endothelial cells from wild type hhex mutants and hhex overexpression zebrafish embryos", "GSE111963", "Transcriptome Analysis", "We used high throughput sequencing to identify differential expression in siblings hhex mutants and hhex overexpression endothelial cells at 48 hpf. Overall design: FACS sorted endothelial cells from siblings hhex mutants and hhex overexpression at 48 hpf", null, "pubmed:30006544", null, "hhex overexpression rep2", "GSM3045716", null, "tissue:FACS sorted endothelial cells|genotype/variation:hhex overexpression|age:48 hpf|strain:AB|cell type:endothelial cells", "hhex overexpression rep2", "The resulting raw reads were assessed for quality adapter content and duplication rates with FastQC Andrews S. 2010 FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides Davis et al. Kraken: A set of tools for quality control and analysis of high throughput sequence data. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter \u201c outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10% Dobin et al. STAR: ultrafast universal RNA seq aligner. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.62 Love et al. Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Only genes with a minimum fold change of + 1.5 log2 + 0.59 a maximum Benjamini Hochberg corrected p value of 0.05 and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers Activities at the Universal Protein Resource UniProt. Genome build: DanCer10 GRCz10.87 Supplementary files format and content: tab delimited text files include library size normlized counts per peak", "FACS sorted endothelial cells", null, "For isolating endothelial cells from Tgkdrl:EGFPs843 siblings and Tgkdrl:EGFPs843 hhex mutant at 48 hpf embryos were divided based on the absence of PLs. Then embryos were rinsed in HBSS Gibco followed by dissociation in TrypLE express Gibco at 28\u00b0C with repeated pipetting. Endothelial cells were isolated using BD Aria sorter and sorted for EGFP+ or tdTomato+/EGFP+ signals for Tgkdrl:EGFPs843 Tgfli1a:tdTomato 2A hhexbns136. RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. 6ng total RNA was used as input for SMARTer\u00ae Stranded Total RNA Seq Kit Pico Input Mammalian Kit Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry resulting in minimum of 30M reads per library with 1x75bp single end setup.", null, "genotype/variation:hhex overexpression|age:48 hpf|strain:AB|cell type:endothelial cells", "GSM3045716", "GSM3045716: hhex overexpression rep2; Danio rerio; RNA Seq", "GSM3045716", null, "1", "For isolating endothelial cells from Tgkdrl:EGFPs843 siblings and Tgkdrl:EGFPs843 hhex mutant at 48 hpf embryos were divided based on the absence of PLs. Then embryos were rinsed in HBSS Gibco followed by dissociation in TrypLE express Gibco at 28\u00b0C with repeated pipetting. Endothelial cells were isolated using BD Aria sorter and sorted for EGFP+ or tdTomato+/EGFP+ signals for Tgkdrl:EGFPs843 Tgfli1a:tdTomato 2A hhexbns136. RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. 6ng total RNA was used as input for SMARTer\u00ae Stranded Total RNA Seq Kit Pico Input Mammalian Kit Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry resulting in minimum of 30M reads per library with 1x75bp single end setup.", "GEO Accession:GSM3045716", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP135898", null, null, "Sebastien_OE_2_R1.fastq.gz", "fastq", 2514724985.0, 34768823.0, "GSM3045716 r1", "0:72.33 1:0", "A:565805246;C:704077993;G:741187599;T:503446013;N:208134", 72, 0, null, null, 565805246, 704077993, 741187599, 503446013, 208134, "SRX3803619", "SRS3055252", "SRA667127", "GEO", "MPI for heart and lung research", 1, 0.94763, null, 0.26354, null, 0.80702, null, 0.62768, null, 74, null, "B", null, "usable mapping rate", "illumina", "nextseq", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "Germany", "2018-03-16", "Hatching", "Embryo", "Endothelium", "Cardiovascular System"], [47741, "SRR6848348", "SRX3803618", "SRS3055251", "SRP135898", "PRJNA438687", "Transcriptome profiling of endothelial cells from wild type hhex mutants and hhex overexpression zebrafish embryos", "GSE111963", "Transcriptome Analysis", "We used high throughput sequencing to identify differential expression in siblings hhex mutants and hhex overexpression endothelial cells at 48 hpf. Overall design: FACS sorted endothelial cells from siblings hhex mutants and hhex overexpression at 48 hpf", null, "pubmed:30006544", null, "hhex overexpression rep1", "GSM3045715", null, "tissue:FACS sorted endothelial cells|genotype/variation:hhex overexpression|age:48 hpf|strain:AB|cell type:endothelial cells", "hhex overexpression rep1", "The resulting raw reads were assessed for quality adapter content and duplication rates with FastQC Andrews S. 2010 FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides Davis et al. Kraken: A set of tools for quality control and analysis of high throughput sequence data. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter \u201c outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10% Dobin et al. STAR: ultrafast universal RNA seq aligner. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.62 Love et al. Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Only genes with a minimum fold change of + 1.5 log2 + 0.59 a maximum Benjamini Hochberg corrected p value of 0.05 and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers Activities at the Universal Protein Resource UniProt. Genome build: DanCer10 GRCz10.87 Supplementary files format and content: tab delimited text files include library size normlized counts per peak", "FACS sorted endothelial cells", null, "For isolating endothelial cells from Tgkdrl:EGFPs843 siblings and Tgkdrl:EGFPs843 hhex mutant at 48 hpf embryos were divided based on the absence of PLs. Then embryos were rinsed in HBSS Gibco followed by dissociation in TrypLE express Gibco at 28\u00b0C with repeated pipetting. Endothelial cells were isolated using BD Aria sorter and sorted for EGFP+ or tdTomato+/EGFP+ signals for Tgkdrl:EGFPs843 Tgfli1a:tdTomato 2A hhexbns136. RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. 6ng total RNA was used as input for SMARTer\u00ae Stranded Total RNA Seq Kit Pico Input Mammalian Kit Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry resulting in minimum of 30M reads per library with 1x75bp single end setup.", null, "genotype/variation:hhex overexpression|age:48 hpf|strain:AB|cell type:endothelial cells", "GSM3045715", "GSM3045715: hhex overexpression rep1; Danio rerio; RNA Seq", "GSM3045715", null, "1", "For isolating endothelial cells from Tgkdrl:EGFPs843 siblings and Tgkdrl:EGFPs843 hhex mutant at 48 hpf embryos were divided based on the absence of PLs. Then embryos were rinsed in HBSS Gibco followed by dissociation in TrypLE express Gibco at 28\u00b0C with repeated pipetting. Endothelial cells were isolated using BD Aria sorter and sorted for EGFP+ or tdTomato+/EGFP+ signals for Tgkdrl:EGFPs843 Tgfli1a:tdTomato 2A hhexbns136. RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. 6ng total RNA was used as input for SMARTer\u00ae Stranded Total RNA Seq Kit Pico Input Mammalian Kit Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry resulting in minimum of 30M reads per library with 1x75bp single end setup.", "GEO Accession:GSM3045715", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP135898", null, null, "Sebastien_OE_1_R1.fastq.gz", "fastq", 2201523348.0, 30479961.0, "GSM3045715 r1", "0:72.23 1:0", "A:510844407;C:602803512;G:634953285;T:452682176;N:239968", 72, 0, null, null, 510844407, 602803512, 634953285, 452682176, 239968, "SRX3803618", "SRS3055251", "SRA667127", "GEO", "MPI for heart and lung research", 1, 0.94219, null, 0.27653, null, 0.80466, null, 0.66516, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "Germany", "2018-03-16", "Hatching", "Embryo", "Endothelium", "Cardiovascular System"], [47742, "SRR6848347", "SRX3803617", "SRS3055250", "SRP135898", "PRJNA438687", "Transcriptome profiling of endothelial cells from wild type hhex mutants and hhex overexpression zebrafish embryos", "GSE111963", "Transcriptome Analysis", "We used high throughput sequencing to identify differential expression in siblings hhex mutants and hhex overexpression endothelial cells at 48 hpf. Overall design: FACS sorted endothelial cells from siblings hhex mutants and hhex overexpression at 48 hpf", null, "pubmed:30006544", null, "hhex mutant rep2", "GSM3045714", null, "tissue:FACS sorted endothelial cells|genotype/variation:hhex mutant|age:48 hpf|strain:AB|cell type:endothelial cells", "hhex mutant rep2", "The resulting raw reads were assessed for quality adapter content and duplication rates with FastQC Andrews S. 2010 FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides Davis et al. Kraken: A set of tools for quality control and analysis of high throughput sequence data. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter \u201c outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10% Dobin et al. STAR: ultrafast universal RNA seq aligner. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.62 Love et al. Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Only genes with a minimum fold change of + 1.5 log2 + 0.59 a maximum Benjamini Hochberg corrected p value of 0.05 and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers Activities at the Universal Protein Resource UniProt. Genome build: DanCer10 GRCz10.87 Supplementary files format and content: tab delimited text files include library size normlized counts per peak", "FACS sorted endothelial cells", null, "For isolating endothelial cells from Tgkdrl:EGFPs843 siblings and Tgkdrl:EGFPs843 hhex mutant at 48 hpf embryos were divided based on the absence of PLs. Then embryos were rinsed in HBSS Gibco followed by dissociation in TrypLE express Gibco at 28\u00b0C with repeated pipetting. Endothelial cells were isolated using BD Aria sorter and sorted for EGFP+ or tdTomato+/EGFP+ signals for Tgkdrl:EGFPs843 Tgfli1a:tdTomato 2A hhexbns136. RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. 6ng total RNA was used as input for SMARTer\u00ae Stranded Total RNA Seq Kit Pico Input Mammalian Kit Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry resulting in minimum of 30M reads per library with 1x75bp single end setup.", null, "genotype/variation:hhex mutant|age:48 hpf|strain:AB|cell type:endothelial cells", "GSM3045714", "GSM3045714: hhex mutant rep2; Danio rerio; RNA Seq", "GSM3045714", null, "1", "For isolating endothelial cells from Tgkdrl:EGFPs843 siblings and Tgkdrl:EGFPs843 hhex mutant at 48 hpf embryos were divided based on the absence of PLs. Then embryos were rinsed in HBSS Gibco followed by dissociation in TrypLE express Gibco at 28\u00b0C with repeated pipetting. Endothelial cells were isolated using BD Aria sorter and sorted for EGFP+ or tdTomato+/EGFP+ signals for Tgkdrl:EGFPs843 Tgfli1a:tdTomato 2A hhexbns136. RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. 6ng total RNA was used as input for SMARTer\u00ae Stranded Total RNA Seq Kit Pico Input Mammalian Kit Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry resulting in minimum of 30M reads per library with 1x75bp single end setup.", "GEO Accession:GSM3045714", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP135898", null, null, "Sebastien_Mut_2_R1.fastq.gz", "fastq", 2377033794.0, 32865413.0, "GSM3045714 r1", "0:72.33 1:0", "A:531221225;C:668093793;G:704926379;T:472544720;N:247677", 72, 0, null, null, 531221225, 668093793, 704926379, 472544720, 247677, "SRX3803617", "SRS3055250", "SRA667127", "GEO", "MPI for heart and lung research", 1, 0.93202, null, 0.25789, null, 0.81617, null, 0.66408, null, 74, null, "B", null, "usable mapping rate", "illumina", "nextseq", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "Germany", "2018-03-16", "Hatching", "Embryo", "Endothelium", "Cardiovascular System"], [47743, "SRR6848346", "SRX3803616", "SRS3055249", "SRP135898", "PRJNA438687", "Transcriptome profiling of endothelial cells from wild type hhex mutants and hhex overexpression zebrafish embryos", "GSE111963", "Transcriptome Analysis", "We used high throughput sequencing to identify differential expression in siblings hhex mutants and hhex overexpression endothelial cells at 48 hpf. Overall design: FACS sorted endothelial cells from siblings hhex mutants and hhex overexpression at 48 hpf", null, "pubmed:30006544", null, "hhex mutant rep1", "GSM3045713", null, "tissue:FACS sorted endothelial cells|genotype/variation:hhex mutant|age:48 hpf|strain:AB|cell type:endothelial cells", "hhex mutant rep1", "The resulting raw reads were assessed for quality adapter content and duplication rates with FastQC Andrews S. 2010 FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides Davis et al. Kraken: A set of tools for quality control and analysis of high throughput sequence data. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter \u201c outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10% Dobin et al. STAR: ultrafast universal RNA seq aligner. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.62 Love et al. Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Only genes with a minimum fold change of + 1.5 log2 + 0.59 a maximum Benjamini Hochberg corrected p value of 0.05 and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers Activities at the Universal Protein Resource UniProt. Genome build: DanCer10 GRCz10.87 Supplementary files format and content: tab delimited text files include library size normlized counts per peak", "FACS sorted endothelial cells", null, "For isolating endothelial cells from Tgkdrl:EGFPs843 siblings and Tgkdrl:EGFPs843 hhex mutant at 48 hpf embryos were divided based on the absence of PLs. Then embryos were rinsed in HBSS Gibco followed by dissociation in TrypLE express Gibco at 28\u00b0C with repeated pipetting. Endothelial cells were isolated using BD Aria sorter and sorted for EGFP+ or tdTomato+/EGFP+ signals for Tgkdrl:EGFPs843 Tgfli1a:tdTomato 2A hhexbns136. RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. 6ng total RNA was used as input for SMARTer\u00ae Stranded Total RNA Seq Kit Pico Input Mammalian Kit Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry resulting in minimum of 30M reads per library with 1x75bp single end setup.", null, "genotype/variation:hhex mutant|age:48 hpf|strain:AB|cell type:endothelial cells", "GSM3045713", "GSM3045713: hhex mutant rep1; Danio rerio; RNA Seq", "GSM3045713", null, "1", "For isolating endothelial cells from Tgkdrl:EGFPs843 siblings and Tgkdrl:EGFPs843 hhex mutant at 48 hpf embryos were divided based on the absence of PLs. Then embryos were rinsed in HBSS Gibco followed by dissociation in TrypLE express Gibco at 28\u00b0C with repeated pipetting. Endothelial cells were isolated using BD Aria sorter and sorted for EGFP+ or tdTomato+/EGFP+ signals for Tgkdrl:EGFPs843 Tgfli1a:tdTomato 2A hhexbns136. RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. 6ng total RNA was used as input for SMARTer\u00ae Stranded Total RNA Seq Kit Pico Input Mammalian Kit Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry resulting in minimum of 30M reads per library with 1x75bp single end setup.", "GEO Accession:GSM3045713", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP135898", null, null, "Sebastien_Mut_1_R1.fastq.gz", "fastq", 2492708175.0, 34527636.0, "GSM3045713 r1", "0:72.19 1:0", "A:555859455;C:702003394;G:740775583;T:493818885;N:250858", 72, 0, null, null, 555859455, 702003394, 740775583, 493818885, 250858, "SRX3803616", "SRS3055249", "SRA667127", "GEO", "MPI for heart and lung research", 1, 0.93924, null, 0.25343, null, 0.81889, null, 0.6311, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "Germany", "2018-03-16", "Hatching", "Embryo", "Endothelium", "Cardiovascular System"], [47744, "SRR6848345", "SRX3803615", "SRS3055248", "SRP135898", "PRJNA438687", "Transcriptome profiling of endothelial cells from wild type hhex mutants and hhex overexpression zebrafish embryos", "GSE111963", "Transcriptome Analysis", "We used high throughput sequencing to identify differential expression in siblings hhex mutants and hhex overexpression endothelial cells at 48 hpf. Overall design: FACS sorted endothelial cells from siblings hhex mutants and hhex overexpression at 48 hpf", null, "pubmed:30006544", null, "Sibling rep2", "GSM3045712", null, "tissue:FACS sorted endothelial cells|genotype/variation:wild type|age:48 hpf|strain:AB|cell type:endothelial cells", "Sibling rep2", "The resulting raw reads were assessed for quality adapter content and duplication rates with FastQC Andrews S. 2010 FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides Davis et al. Kraken: A set of tools for quality control and analysis of high throughput sequence data. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter \u201c outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10% Dobin et al. STAR: ultrafast universal RNA seq aligner. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.62 Love et al. Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Only genes with a minimum fold change of + 1.5 log2 + 0.59 a maximum Benjamini Hochberg corrected p value of 0.05 and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers Activities at the Universal Protein Resource UniProt. Genome build: DanCer10 GRCz10.87 Supplementary files format and content: tab delimited text files include library size normlized counts per peak", "FACS sorted endothelial cells", null, "For isolating endothelial cells from Tgkdrl:EGFPs843 siblings and Tgkdrl:EGFPs843 hhex mutant at 48 hpf embryos were divided based on the absence of PLs. Then embryos were rinsed in HBSS Gibco followed by dissociation in TrypLE express Gibco at 28\u00b0C with repeated pipetting. Endothelial cells were isolated using BD Aria sorter and sorted for EGFP+ or tdTomato+/EGFP+ signals for Tgkdrl:EGFPs843 Tgfli1a:tdTomato 2A hhexbns136. RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. 6ng total RNA was used as input for SMARTer\u00ae Stranded Total RNA Seq Kit Pico Input Mammalian Kit Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry resulting in minimum of 30M reads per library with 1x75bp single end setup.", null, "genotype/variation:wild type|age:48 hpf|strain:AB|cell type:endothelial cells", "GSM3045712", "GSM3045712: Sibling rep2; Danio rerio; RNA Seq", "GSM3045712", null, "1", "For isolating endothelial cells from Tgkdrl:EGFPs843 siblings and Tgkdrl:EGFPs843 hhex mutant at 48 hpf embryos were divided based on the absence of PLs. Then embryos were rinsed in HBSS Gibco followed by dissociation in TrypLE express Gibco at 28\u00b0C with repeated pipetting. Endothelial cells were isolated using BD Aria sorter and sorted for EGFP+ or tdTomato+/EGFP+ signals for Tgkdrl:EGFPs843 Tgfli1a:tdTomato 2A hhexbns136. RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. 6ng total RNA was used as input for SMARTer\u00ae Stranded Total RNA Seq Kit Pico Input Mammalian Kit Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry resulting in minimum of 30M reads per library with 1x75bp single end setup.", "GEO Accession:GSM3045712", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP135898", null, null, "Sebastien_WT_2_R1.fastq.gz", "fastq", 2451974351.0, 33830383.0, "GSM3045712 r1", "0:72.48 1:0", "A:557370317;C:679644672;G:720300776;T:494468929;N:189657", 72, 0, null, null, 557370317, 679644672, 720300776, 494468929, 189657, "SRX3803615", "SRS3055248", "SRA667127", "GEO", "MPI for heart and lung research", 1, 0.91674, null, 0.25327, null, 0.80868, null, 0.70337, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "Germany", "2018-03-16", "Hatching", "Embryo", "Endothelium", "Cardiovascular System"], [47745, "SRR6848344", "SRX3803614", "SRS3055247", "SRP135898", "PRJNA438687", "Transcriptome profiling of endothelial cells from wild type hhex mutants and hhex overexpression zebrafish embryos", "GSE111963", "Transcriptome Analysis", "We used high throughput sequencing to identify differential expression in siblings hhex mutants and hhex overexpression endothelial cells at 48 hpf. Overall design: FACS sorted endothelial cells from siblings hhex mutants and hhex overexpression at 48 hpf", null, "pubmed:30006544", null, "Sibling rep1", "GSM3045711", null, "tissue:FACS sorted endothelial cells|genotype/variation:wild type|age:48 hpf|strain:AB|cell type:endothelial cells", "Sibling rep1", "The resulting raw reads were assessed for quality adapter content and duplication rates with FastQC Andrews S. 2010 FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides Davis et al. Kraken: A set of tools for quality control and analysis of high throughput sequence data. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter \u201c outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10% Dobin et al. STAR: ultrafast universal RNA seq aligner. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package Liao et al. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.62 Love et al. Moderated estimation of fold change and dispersion for RNA Seq data with DESeq2. Only genes with a minimum fold change of + 1.5 log2 + 0.59 a maximum Benjamini Hochberg corrected p value of 0.05 and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers Activities at the Universal Protein Resource UniProt. Genome build: DanCer10 GRCz10.87 Supplementary files format and content: tab delimited text files include library size normlized counts per peak", "FACS sorted endothelial cells", null, "For isolating endothelial cells from Tgkdrl:EGFPs843 siblings and Tgkdrl:EGFPs843 hhex mutant at 48 hpf embryos were divided based on the absence of PLs. Then embryos were rinsed in HBSS Gibco followed by dissociation in TrypLE express Gibco at 28\u00b0C with repeated pipetting. Endothelial cells were isolated using BD Aria sorter and sorted for EGFP+ or tdTomato+/EGFP+ signals for Tgkdrl:EGFPs843 Tgfli1a:tdTomato 2A hhexbns136. RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. 6ng total RNA was used as input for SMARTer\u00ae Stranded Total RNA Seq Kit Pico Input Mammalian Kit Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry resulting in minimum of 30M reads per library with 1x75bp single end setup.", null, "genotype/variation:wild type|age:48 hpf|strain:AB|cell type:endothelial cells", "GSM3045711", "GSM3045711: Sibling rep1; Danio rerio; RNA Seq", "GSM3045711", null, "1", "For isolating endothelial cells from Tgkdrl:EGFPs843 siblings and Tgkdrl:EGFPs843 hhex mutant at 48 hpf embryos were divided based on the absence of PLs. Then embryos were rinsed in HBSS Gibco followed by dissociation in TrypLE express Gibco at 28\u00b0C with repeated pipetting. Endothelial cells were isolated using BD Aria sorter and sorted for EGFP+ or tdTomato+/EGFP+ signals for Tgkdrl:EGFPs843 Tgfli1a:tdTomato 2A hhexbns136. RNA was isolated using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. 6ng total RNA was used as input for SMARTer\u00ae Stranded Total RNA Seq Kit Pico Input Mammalian Kit Clontech. Sequencing was performed on the NextSeq500 instrument Illumina using v2 chemistry resulting in minimum of 30M reads per library with 1x75bp single end setup.", "GEO Accession:GSM3045711", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP135898", null, null, "Sebastien_WT_1_R1.fastq.gz", "fastq", 2685019288.0, 37185023.0, "GSM3045711 r1", "0:72.21 1:0", "A:629322492;C:731250924;G:769793846;T:554311522;N:340504", 72, 0, null, null, 629322492, 731250924, 769793846, 554311522, 340504, "SRX3803614", "SRS3055247", "SRA667127", "GEO", "MPI for heart and lung research", 1, 0.90551, null, 0.24697, null, 0.80695, null, 0.65765, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "Germany", "2018-03-16", "Hatching", "Embryo", "Endothelium", "Cardiovascular System"], [50604, "SRR8169175", "SRX4989831", "SRS4025849", "SRP168005", "PRJNA504385", "Endothelial transcriptome of 1dpf Zebrafish empryo", "PRJNA504385", "Other", "The study aimed to identify endothelial specific transcript isoforms in 24hpf zebrafish embryo. The polyA RNA sequencing was performed on Illumina GA II platform.", null, null, null, "Endothelial cells", "EC", null, "strain:Tgfli1:EGFP gata1a: dsRed|age:1 dpf stage:1 dpf applicable|tissue:Endothelium|cell type:Endothelial|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Endothelial cells", "EC", "EC", "PolyA RNA Seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP168005", null, null, "EC_R1.fastq EC_R2.fastq", "fastq fastq", 3373890496.0, 22196648.0, "EC R1.fastq", "0:76 1:76", "A:984631808;C:769706826;G:812424195;T:790813473;N:16314194", 76, 76, null, null, 984631808, 769706826, 812424195, 790813473, 16314194, "SRX4989831", "SRS4025849", "SRA805845", "CSIR-Institute of Genomics and Integrative Biology|GN Ramachandran Knowledge Center", "CSIR-Institute of Genomics and Integrative Biology", 2, 0.92323, 0.92543, 0.07989, 0.0849, 0.76842, 0.77964, 0.46181, 0.47429, 76, 76, "B", "B", "biological fallback assumption", "illumina", "early_illumina", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "India", "2019-12-06", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [50605, "SRR8169176", "SRX4989830", "SRS4025850", "SRP168005", "PRJNA504385", "Endothelial transcriptome of 1dpf Zebrafish empryo", "PRJNA504385", "Other", "The study aimed to identify endothelial specific transcript isoforms in 24hpf zebrafish embryo. The polyA RNA sequencing was performed on Illumina GA II platform.", null, null, null, "Non endothelial cells", "NEC", null, "strain:Tgfli1:EGFP gata1a: dsRed|age:1 dpf stage:1 dpf applicable|tissue:Whole organism devoid of endothelium|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Non endothelial cells", "NEC", "NEC", "PolyA RNA Seq", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP168005", null, null, "NEC_R2.fastq NEC_R1.fastq", "fastq fastq", 3903685432.0, 25682141.0, "NEC R1.fastq", "0:76 1:76", "A:1078599801;C:913868400;G:942281029;T:950473482;N:18462720", 76, 76, null, null, 1078599801, 913868400, 942281029, 950473482, 18462720, "SRX4989830", "SRS4025850", "SRA805845", "CSIR-Institute of Genomics and Integrative Biology|GN Ramachandran Knowledge Center", "CSIR-Institute of Genomics and Integrative Biology", 2, 0.93037, 0.92641, 0.10373, 0.11231, 0.72644, 0.74081, 0.48329, 0.48409, 76, 76, "B", "B", "biological fallback assumption", "illumina", "early_illumina", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "India", "2019-12-06", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [52764, "SRR9207199", "SRX5978265", "SRS4884520", "SRP200560", "PRJNA547066", "RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf", "GSE132259", "Transcriptome Analysis", "The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.", "parent bioproject:PRJNA546805", "pubmed:31395869", null, "RNA seq MO DP R1hi rep3", "GSM3855057", null, "source name:haemogenic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:runx1 morpholino injected", "RNA seq MO DP R1hi rep3", "Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value.", "haemogenic endothelium", "double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf.", "age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:runx1 morpholino injected", "GSM3855057", "GSM3855057: MO DP R1hi rep3; Danio rerio; RNA Seq", "GSM3855057", null, "1", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "GEO Accession:GSM3855057", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP200560", null, null, "WTCHG_236896_268_1_pair.fq.gz WTCHG_236896_268_2_pair.fq.gz", "fastq fastq", 1927186907.0, 13135764.0, "GSM3855057 r1", "0:74.85 1:71.86", "A:495349382;C:442938837;G:459765161;T:529104158;N:29369", 74, 71, null, null, 495349382, 442938837, 459765161, 529104158, 29369, "SRX5978265", "SRS4884520", "SRA894667", "GEO", "Oxford University", 2, 0.9511, 0.71957, 0.05876, 0.04975, 0.80322, 0.83463, 0.41847, 0.47909, 75, 64, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-06-05", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [52765, "SRR9207200", "SRX5978265", "SRS4884520", "SRP200560", "PRJNA547066", "RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf", "GSE132259", "Transcriptome Analysis", "The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.", "parent bioproject:PRJNA546805", "pubmed:31395869", null, "RNA seq MO DP R1hi rep3", "GSM3855057", null, "source name:haemogenic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:runx1 morpholino injected", "RNA seq MO DP R1hi rep3", "Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value.", "haemogenic endothelium", "double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf.", "age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:runx1 morpholino injected", "GSM3855057", "GSM3855057: MO DP R1hi rep3; Danio rerio; RNA Seq", "GSM3855057", null, "1", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "GEO Accession:GSM3855057", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP200560", null, null, "WTCHG_236897_268_1_pair.fq.gz WTCHG_236897_268_2_pair.fq.gz", "fastq fastq", 1909528693.0, 13017658.0, "GSM3855057 r2", "0:74.82 1:71.87", "A:490710971;C:436487071;G:453444216;T:528853285;N:33150", 74, 71, null, null, 490710971, 436487071, 453444216, 528853285, 33150, "SRX5978265", "SRS4884520", "SRA894667", "GEO", "Oxford University", 2, 0.94988, 0.70903, 0.05941, 0.04918, 0.80346, 0.83597, 0.42243, 0.48127, 74, 69, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-06-05", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [52766, "SRR9207197", "SRX5978264", "SRS4884519", "SRP200560", "PRJNA547066", "RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf", "GSE132259", "Transcriptome Analysis", "The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.", "parent bioproject:PRJNA546805", "pubmed:31395869", null, "RNA seq MO DP R1hi rep2", "GSM3855056", null, "source name:haemogenic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:runx1 morpholino injected", "RNA seq MO DP R1hi rep2", "Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value.", "haemogenic endothelium", "double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf.", "age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:runx1 morpholino injected", "GSM3855056", "GSM3855056: MO DP R1hi rep2; Danio rerio; RNA Seq", "GSM3855056", null, "1", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "GEO Accession:GSM3855056", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP200560", null, null, "WTCHG_236896_253_2_pair.fq.gz WTCHG_236896_253_1_pair.fq.gz", "fastq fastq", 2328318316.0, 15846855.0, "GSM3855056 r1", "0:74.86 1:72.07", "A:595900608;C:546479100;G:562297908;T:623605072;N:35628", 74, 72, null, null, 595900608, 546479100, 562297908, 623605072, 35628, "SRX5978264", "SRS4884519", "SRA894667", "GEO", "Oxford University", 2, 0.95426, 0.78099, 0.04531, 0.04107, 0.79285, 0.81738, 0.47636, 0.47393, 74, 74, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-06-05", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [52767, "SRR9207198", "SRX5978264", "SRS4884519", "SRP200560", "PRJNA547066", "RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf", "GSE132259", "Transcriptome Analysis", "The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.", "parent bioproject:PRJNA546805", "pubmed:31395869", null, "RNA seq MO DP R1hi rep2", "GSM3855056", null, "source name:haemogenic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:runx1 morpholino injected", "RNA seq MO DP R1hi rep2", "Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value.", "haemogenic endothelium", "double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf.", "age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:runx1 morpholino injected", "GSM3855056", "GSM3855056: MO DP R1hi rep2; Danio rerio; RNA Seq", "GSM3855056", null, "1", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "GEO Accession:GSM3855056", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP200560", null, null, "WTCHG_236897_253_1_pair.fq.gz WTCHG_236897_253_2_pair.fq.gz", "fastq fastq", 2302889916.0, 15678935.0, "GSM3855056 r2", "0:74.83 1:72.05", "A:589414837;C:537423117;G:553631542;T:622379721;N:40699", 74, 72, null, null, 589414837, 537423117, 553631542, 622379721, 40699, "SRX5978264", "SRS4884519", "SRA894667", "GEO", "Oxford University", 2, 0.95316, 0.76729, 0.04543, 0.04, 0.79368, 0.81994, 0.4793, 0.45619, 74, 73, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-06-05", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [52768, "SRR9207195", "SRX5978263", "SRS4884518", "SRP200560", "PRJNA547066", "RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf", "GSE132259", "Transcriptome Analysis", "The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.", "parent bioproject:PRJNA546805", "pubmed:31395869", null, "RNA seq MO DP R1hi rep1", "GSM3855055", null, "source name:haemogenic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:runx1 morpholino injected", "RNA seq MO DP R1hi rep1", "Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value.", "haemogenic endothelium", "double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf.", "age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:runx1 morpholino injected", "GSM3855055", "GSM3855055: MO DP R1hi rep1; Danio rerio; RNA Seq", "GSM3855055", null, "1", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "GEO Accession:GSM3855055", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP200560", null, null, "WTCHG_236896_246_1_pair.fq.gz WTCHG_236896_246_2_pair.fq.gz", "fastq fastq", 2117580563.0, 14386411.0, "GSM3855055 r1", "0:74.87 1:72.33", "A:541407670;C:500318189;G:514959635;T:560861522;N:33547", 74, 72, null, null, 541407670, 500318189, 514959635, 560861522, 33547, "SRX5978263", "SRS4884518", "SRA894667", "GEO", "Oxford University", 2, 0.95698, 0.79806, 0.0412, 0.03838, 0.79683, 0.82073, 0.4361, 0.47246, 75, 74, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-06-05", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [52769, "SRR9207196", "SRX5978263", "SRS4884518", "SRP200560", "PRJNA547066", "RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf", "GSE132259", "Transcriptome Analysis", "The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.", "parent bioproject:PRJNA546805", "pubmed:31395869", null, "RNA seq MO DP R1hi rep1", "GSM3855055", null, "source name:haemogenic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:runx1 morpholino injected", "RNA seq MO DP R1hi rep1", "Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value.", "haemogenic endothelium", "double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf.", "age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:runx1 morpholino injected", "GSM3855055", "GSM3855055: MO DP R1hi rep1; Danio rerio; RNA Seq", "GSM3855055", null, "1", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "GEO Accession:GSM3855055", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP200560", null, null, "WTCHG_236897_246_1_pair.fq.gz WTCHG_236897_246_2_pair.fq.gz", "fastq fastq", 2093566860.0, 14226227.0, "GSM3855055 r2", "0:74.83 1:72.33", "A:535219614;C:492666345;G:507484718;T:558158640;N:37543", 74, 72, null, null, 535219614, 492666345, 507484718, 558158640, 37543, "SRX5978263", "SRS4884518", "SRA894667", "GEO", "Oxford University", 2, 0.95586, 0.7889, 0.04114, 0.03868, 0.79689, 0.82104, 0.43998, 0.46953, 74, 47, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-06-05", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [52770, "SRR9207193", "SRX5978262", "SRS4884517", "SRP200560", "PRJNA547066", "RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf", "GSE132259", "Transcriptome Analysis", "The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.", "parent bioproject:PRJNA546805", "pubmed:31395869", null, "RNA seq MO DN rep3", "GSM3855054", null, "source name:non endothelial tissue|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:runx1 morpholino injected", "RNA seq MO DN rep3", "Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value.", "non endothelial tissue", "double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf.", "age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:runx1 morpholino injected", "GSM3855054", "GSM3855054: MO DN rep3; Danio rerio; RNA Seq", "GSM3855054", null, "1", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "GEO Accession:GSM3855054", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP200560", null, null, "WTCHG_236896_269_1_pair.fq.gz WTCHG_236896_269_2_pair.fq.gz", "fastq fastq", 2046617161.0, 13945847.0, "GSM3855054 r1", "0:74.83 1:71.93", "A:534129043;C:466415284;G:478200001;T:567840465;N:32368", 74, 71, null, null, 534129043, 466415284, 478200001, 567840465, 32368, "SRX5978262", "SRS4884517", "SRA894667", "GEO", "Oxford University", 2, 0.94896, 0.77373, 0.08658, 0.07153, 0.73519, 0.76715, 0.49305, 0.48341, 75, 74, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-06-05", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [52771, "SRR9207194", "SRX5978262", "SRS4884517", "SRP200560", "PRJNA547066", "RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf", "GSE132259", "Transcriptome Analysis", "The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.", "parent bioproject:PRJNA546805", "pubmed:31395869", null, "RNA seq MO DN rep3", "GSM3855054", null, "source name:non endothelial tissue|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:runx1 morpholino injected", "RNA seq MO DN rep3", "Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value.", "non endothelial tissue", "double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf.", "age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:runx1 morpholino injected", "GSM3855054", "GSM3855054: MO DN rep3; Danio rerio; RNA Seq", "GSM3855054", null, "1", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "GEO Accession:GSM3855054", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP200560", null, null, "WTCHG_236897_269_1_pair.fq.gz WTCHG_236897_269_2_pair.fq.gz", "fastq fastq", 2013937570.0, 13725739.0, "GSM3855054 r2", "0:74.79 1:71.93", "A:525460437;C:456678849;G:468917277;T:562845673;N:35334", 74, 71, null, null, 525460437, 456678849, 468917277, 562845673, 35334, "SRX5978262", "SRS4884517", "SRA894667", "GEO", "Oxford University", 2, 0.94917, 0.76456, 0.08857, 0.07125, 0.73541, 0.76777, 0.49906, 0.49093, 74, 44, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-06-05", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [52772, "SRR9207191", "SRX5978261", "SRS4884516", "SRP200560", "PRJNA547066", "RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf", "GSE132259", "Transcriptome Analysis", "The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.", "parent bioproject:PRJNA546805", "pubmed:31395869", null, "RNA seq MO DN rep2", "GSM3855053", null, "source name:non endothelial tissue|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:runx1 morpholino injected", "RNA seq MO DN rep2", "Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value.", "non endothelial tissue", "double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf.", "age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:runx1 morpholino injected", "GSM3855053", "GSM3855053: MO DN rep2; Danio rerio; RNA Seq", "GSM3855053", null, "1", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "GEO Accession:GSM3855053", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP200560", null, null, "WTCHG_236896_254_1_pair.fq.gz WTCHG_236896_254_2_pair.fq.gz", "fastq fastq", 2491569443.0, 17007413.0, "GSM3855053 r1", "0:74.84 1:71.66", "A:650887336;C:562551977;G:579971830;T:698120812;N:37488", 74, 71, null, null, 650887336, 562551977, 579971830, 698120812, 37488, "SRX5978261", "SRS4884516", "SRA894667", "GEO", "Oxford University", 2, 0.95058, 0.74758, 0.08565, 0.06922, 0.74817, 0.78344, 0.49706, 0.48533, 74, 74, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-06-05", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [52773, "SRR9207192", "SRX5978261", "SRS4884516", "SRP200560", "PRJNA547066", "RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf", "GSE132259", "Transcriptome Analysis", "The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.", "parent bioproject:PRJNA546805", "pubmed:31395869", null, "RNA seq MO DN rep2", "GSM3855053", null, "source name:non endothelial tissue|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:runx1 morpholino injected", "RNA seq MO DN rep2", "Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value.", "non endothelial tissue", "double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf.", "age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:runx1 morpholino injected", "GSM3855053", "GSM3855053: MO DN rep2; Danio rerio; RNA Seq", "GSM3855053", null, "1", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "GEO Accession:GSM3855053", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP200560", null, null, "WTCHG_236897_254_1_pair.fq.gz WTCHG_236897_254_2_pair.fq.gz", "fastq fastq", 2467826388.0, 16847563.0, "GSM3855053 r2", "0:74.80 1:71.67", "A:644767348;C:554488060;G:572473532;T:696053759;N:43689", 74, 71, null, null, 644767348, 554488060, 572473532, 696053759, 43689, "SRX5978261", "SRS4884516", "SRA894667", "GEO", "Oxford University", 2, 0.95097, 0.73759, 0.0857, 0.0679, 0.74805, 0.78307, 0.50597, 0.48761, 74, 59, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-06-05", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [52774, "SRR9207189", "SRX5978260", "SRS4884515", "SRP200560", "PRJNA547066", "RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf", "GSE132259", "Transcriptome Analysis", "The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.", "parent bioproject:PRJNA546805", "pubmed:31395869", null, "RNA seq MO DN rep1", "GSM3855052", null, "source name:non endothelial tissue|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:runx1 morpholino injected", "RNA seq MO DN rep1", "Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value.", "non endothelial tissue", "double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf.", "age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:runx1 morpholino injected", "GSM3855052", "GSM3855052: MO DN rep1; Danio rerio; RNA Seq", "GSM3855052", null, "1", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "GEO Accession:GSM3855052", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP200560", null, null, "WTCHG_236896_247_1_pair.fq.gz WTCHG_236896_247_2_pair.fq.gz", "fastq fastq", 1764365530.0, 12029530.0, "GSM3855052 r1", "0:74.84 1:71.83", "A:466613214;C:395400217;G:407881798;T:494443051;N:27250", 74, 71, null, null, 466613214, 395400217, 407881798, 494443051, 27250, "SRX5978260", "SRS4884515", "SRA894667", "GEO", "Oxford University", 2, 0.95055, 0.76043, 0.0868, 0.07313, 0.75436, 0.79295, 0.51961, 0.5131, 75, 74, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-06-05", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [52775, "SRR9207190", "SRX5978260", "SRS4884515", "SRP200560", "PRJNA547066", "RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf", "GSE132259", "Transcriptome Analysis", "The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.", "parent bioproject:PRJNA546805", "pubmed:31395869", null, "RNA seq MO DN rep1", "GSM3855052", null, "source name:non endothelial tissue|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:runx1 morpholino injected", "RNA seq MO DN rep1", "Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value.", "non endothelial tissue", "double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf.", "age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:runx1 morpholino injected", "GSM3855052", "GSM3855052: MO DN rep1; Danio rerio; RNA Seq", "GSM3855052", null, "1", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "GEO Accession:GSM3855052", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP200560", null, null, "WTCHG_236897_247_1_pair.fq.gz WTCHG_236897_247_2_pair.fq.gz", "fastq fastq", 1746830974.0, 11912737.0, "GSM3855052 r2", "0:74.80 1:71.83", "A:461791276;C:389648653;G:402516938;T:492843307;N:30800", 74, 71, null, null, 461791276, 389648653, 402516938, 492843307, 30800, "SRX5978260", "SRS4884515", "SRA894667", "GEO", "Oxford University", 2, 0.94945, 0.75002, 0.08645, 0.07146, 0.75564, 0.79247, 0.52424, 0.51007, 74, 74, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-06-05", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [52776, "SRR9207187", "SRX5978259", "SRS4884514", "SRP200560", "PRJNA547066", "RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf", "GSE132259", "Transcriptome Analysis", "The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.", "parent bioproject:PRJNA546805", "pubmed:31395869", null, "RNA seq Wt DP R1hi rep3", "GSM3855051", null, "source name:haemogenic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:non injected", "RNA seq Wt DP R1hi rep3", "Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value.", "haemogenic endothelium", "double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf.", "age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:non injected", "GSM3855051", "GSM3855051: Wt DP R1hi rep3; Danio rerio; RNA Seq", "GSM3855051", null, "1", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "GEO Accession:GSM3855051", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP200560", null, null, "WTCHG_236896_256_1_pair.fq.gz WTCHG_236896_256_2_pair.fq.gz", "fastq fastq", 2404346186.0, 16361688.0, "GSM3855051 r1", "0:74.85 1:72.10", "A:623840845;C:555338266;G:572145582;T:652983438;N:38055", 74, 72, null, null, 623840845, 555338266, 572145582, 652983438, 38055, "SRX5978259", "SRS4884514", "SRA894667", "GEO", "Oxford University", 2, 0.95156, 0.77737, 0.06227, 0.05592, 0.78013, 0.80811, 0.47747, 0.46476, 75, 74, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-06-05", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [52777, "SRR9207188", "SRX5978259", "SRS4884514", "SRP200560", "PRJNA547066", "RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf", "GSE132259", "Transcriptome Analysis", "The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.", "parent bioproject:PRJNA546805", "pubmed:31395869", null, "RNA seq Wt DP R1hi rep3", "GSM3855051", null, "source name:haemogenic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:non injected", "RNA seq Wt DP R1hi rep3", "Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value.", "haemogenic endothelium", "double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf.", "age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:non injected", "GSM3855051", "GSM3855051: Wt DP R1hi rep3; Danio rerio; RNA Seq", "GSM3855051", null, "1", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "GEO Accession:GSM3855051", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP200560", null, null, "WTCHG_236897_256_1_pair.fq.gz WTCHG_236897_256_2_pair.fq.gz", "fastq fastq", 2376933896.0, 16184470.0, "GSM3855051 r2", "0:74.81 1:72.05", "A:616256503;C:545472678;G:562708331;T:652453993;N:42391", 74, 72, null, null, 616256503, 545472678, 562708331, 652453993, 42391, "SRX5978259", "SRS4884514", "SRA894667", "GEO", "Oxford University", 2, 0.95009, 0.76216, 0.06391, 0.05506, 0.78131, 0.81051, 0.48169, 0.4736, 74, 74, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-06-05", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [52778, "SRR9207185", "SRX5978258", "SRS4884513", "SRP200560", "PRJNA547066", "RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf", "GSE132259", "Transcriptome Analysis", "The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.", "parent bioproject:PRJNA546805", "pubmed:31395869", null, "RNA seq Wt DP R1hi rep2", "GSM3855050", null, "source name:haemogenic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:non injected", "RNA seq Wt DP R1hi rep2", "Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value.", "haemogenic endothelium", "double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf.", "age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:non injected", "GSM3855050", "GSM3855050: Wt DP R1hi rep2; Danio rerio; RNA Seq", "GSM3855050", null, "1", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "GEO Accession:GSM3855050", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP200560", null, null, "WTCHG_236896_249_1_pair.fq.gz WTCHG_236896_249_2_pair.fq.gz", "fastq fastq", 2143701223.0, 14577609.0, "GSM3855050 r1", "0:74.85 1:72.21", "A:556710384;C:496467692;G:509166690;T:581322427;N:34030", 74, 72, null, null, 556710384, 496467692, 509166690, 581322427, 34030, "SRX5978258", "SRS4884513", "SRA894667", "GEO", "Oxford University", 2, 0.94754, 0.79028, 0.06346, 0.05688, 0.7811, 0.80754, 0.47106, 0.45364, 75, 74, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-06-05", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [52779, "SRR9207186", "SRX5978258", "SRS4884513", "SRP200560", "PRJNA547066", "RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf", "GSE132259", "Transcriptome Analysis", "The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.", "parent bioproject:PRJNA546805", "pubmed:31395869", null, "RNA seq Wt DP R1hi rep2", "GSM3855050", null, "source name:haemogenic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:non injected", "RNA seq Wt DP R1hi rep2", "Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value.", "haemogenic endothelium", "double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf.", "age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:non injected", "GSM3855050", "GSM3855050: Wt DP R1hi rep2; Danio rerio; RNA Seq", "GSM3855050", null, "1", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "GEO Accession:GSM3855050", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP200560", null, null, "WTCHG_236897_249_1_pair.fq.gz WTCHG_236897_249_2_pair.fq.gz", "fastq fastq", 2117035142.0, 14401911.0, "GSM3855050 r2", "0:74.82 1:72.18", "A:549829321;C:487941130;G:501062541;T:578164319;N:37831", 74, 72, null, null, 549829321, 487941130, 501062541, 578164319, 37831, "SRX5978258", "SRS4884513", "SRA894667", "GEO", "Oxford University", 2, 0.9478, 0.78326, 0.06392, 0.05622, 0.78271, 0.80764, 0.46978, 0.44622, 74, 74, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-06-05", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [52780, "SRR9207183", "SRX5978257", "SRS4884512", "SRP200560", "PRJNA547066", "RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf", "GSE132259", "Transcriptome Analysis", "The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.", "parent bioproject:PRJNA546805", "pubmed:31395869", null, "RNA seq Wt DP R1hi rep1", "GSM3855049", null, "source name:haemogenic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:non injected", "RNA seq Wt DP R1hi rep1", "Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value.", "haemogenic endothelium", "double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf.", "age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:non injected", "GSM3855049", "GSM3855049: Wt DP R1hi rep1; Danio rerio; RNA Seq", "GSM3855049", null, "1", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "GEO Accession:GSM3855049", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP200560", null, null, "WTCHG_236896_242_1_pair.fq.gz WTCHG_236896_242_2_pair.fq.gz", "fastq fastq", 2095674074.0, 14243567.0, "GSM3855049 r1", "0:74.85 1:72.28", "A:541444792;C:489580880;G:501484244;T:563130979;N:33179", 74, 72, null, null, 541444792, 489580880, 501484244, 563130979, 33179, "SRX5978257", "SRS4884512", "SRA894667", "GEO", "Oxford University", 2, 0.95275, 0.80515, 0.0503, 0.0447, 0.78827, 0.81028, 0.47691, 0.47164, 74, 74, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-06-05", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [52781, "SRR9207184", "SRX5978257", "SRS4884512", "SRP200560", "PRJNA547066", "RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf", "GSE132259", "Transcriptome Analysis", "The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.", "parent bioproject:PRJNA546805", "pubmed:31395869", null, "RNA seq Wt DP R1hi rep1", "GSM3855049", null, "source name:haemogenic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:non injected", "RNA seq Wt DP R1hi rep1", "Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value.", "haemogenic endothelium", "double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf.", "age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:haemogenic endothelium|genotype/variation:non injected", "GSM3855049", "GSM3855049: Wt DP R1hi rep1; Danio rerio; RNA Seq", "GSM3855049", null, "1", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "GEO Accession:GSM3855049", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP200560", null, null, "WTCHG_236897_242_1_pair.fq.gz WTCHG_236897_242_2_pair.fq.gz", "fastq fastq", 2063492969.0, 14026048.0, "GSM3855049 r2", "0:74.82 1:72.30", "A:533045811;C:480334040;G:492421855;T:557653783;N:37480", 74, 72, null, null, 533045811, 480334040, 492421855, 557653783, 37480, "SRX5978257", "SRS4884512", "SRA894667", "GEO", "Oxford University", 2, 0.95243, 0.79788, 0.04971, 0.04343, 0.7878, 0.81016, 0.48035, 0.46512, 74, 74, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-06-05", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [52782, "SRR9207181", "SRX5978256", "SRS4884511", "SRP200560", "PRJNA547066", "RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf", "GSE132259", "Transcriptome Analysis", "The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.", "parent bioproject:PRJNA546805", "pubmed:31395869", null, "RNA seq Wt DP R1med rep3", "GSM3855048", null, "source name:aortic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected", "RNA seq Wt DP R1med rep3", "Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value.", "aortic endothelium", "double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf.", "age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected", "GSM3855048", "GSM3855048: Wt DP R1med rep3; Danio rerio; RNA Seq", "GSM3855048", null, "1", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "GEO Accession:GSM3855048", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP200560", null, null, "WTCHG_236896_265_1_pair.fq.gz WTCHG_236896_265_2_pair.fq.gz", "fastq fastq", 1745443128.0, 11892304.0, "GSM3855048 r1", "0:74.86 1:71.91", "A:453150216;C:403838492;G:414952890;T:473474634;N:26896", 74, 71, null, null, 453150216, 403838492, 414952890, 473474634, 26896, "SRX5978256", "SRS4884511", "SRA894667", "GEO", "Oxford University", 2, 0.95301, 0.78351, 0.0658, 0.06097, 0.78368, 0.80941, 0.47251, 0.4445, 75, 74, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-06-05", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [52783, "SRR9207182", "SRX5978256", "SRS4884511", "SRP200560", "PRJNA547066", "RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf", "GSE132259", "Transcriptome Analysis", "The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.", "parent bioproject:PRJNA546805", "pubmed:31395869", null, "RNA seq Wt DP R1med rep3", "GSM3855048", null, "source name:aortic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected", "RNA seq Wt DP R1med rep3", "Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value.", "aortic endothelium", "double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf.", "age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected", "GSM3855048", "GSM3855048: Wt DP R1med rep3; Danio rerio; RNA Seq", "GSM3855048", null, "1", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "GEO Accession:GSM3855048", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP200560", null, null, "WTCHG_236897_265_1_pair.fq.gz WTCHG_236897_265_2_pair.fq.gz", "fastq fastq", 1728817726.0, 11782024.0, "GSM3855048 r2", "0:74.82 1:71.91", "A:448845759;C:398200726;G:409703125;T:472037424;N:30692", 74, 71, null, null, 448845759, 398200726, 409703125, 472037424, 30692, "SRX5978256", "SRS4884511", "SRA894667", "GEO", "Oxford University", 2, 0.9518, 0.77329, 0.06602, 0.05955, 0.78423, 0.81051, 0.47776, 0.46478, 74, 74, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-06-05", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [52784, "SRR9207179", "SRX5978255", "SRS4884510", "SRP200560", "PRJNA547066", "RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf", "GSE132259", "Transcriptome Analysis", "The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.", "parent bioproject:PRJNA546805", "pubmed:31395869", null, "RNA seq Wt DP R1med rep2", "GSM3855047", null, "source name:aortic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected", "RNA seq Wt DP R1med rep2", "Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value.", "aortic endothelium", "double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf.", "age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected", "GSM3855047", "GSM3855047: Wt DP R1med rep2; Danio rerio; RNA Seq", "GSM3855047", null, "1", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "GEO Accession:GSM3855047", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP200560", null, null, "WTCHG_236896_250_1_pair.fq.gz WTCHG_236896_250_2_pair.fq.gz", "fastq fastq", 2096576707.0, 14262609.0, "GSM3855047 r1", "0:74.87 1:72.13", "A:536583711;C:491572815;G:509433296;T:558953949;N:32936", 74, 72, null, null, 536583711, 491572815, 509433296, 558953949, 32936, "SRX5978255", "SRS4884510", "SRA894667", "GEO", "Oxford University", 2, 0.95719, 0.76406, 0.04256, 0.03937, 0.7989, 0.82856, 0.40968, 0.4591, 75, 74, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-06-05", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [52785, "SRR9207180", "SRX5978255", "SRS4884510", "SRP200560", "PRJNA547066", "RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf", "GSE132259", "Transcriptome Analysis", "The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.", "parent bioproject:PRJNA546805", "pubmed:31395869", null, "RNA seq Wt DP R1med rep2", "GSM3855047", null, "source name:aortic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected", "RNA seq Wt DP R1med rep2", "Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value.", "aortic endothelium", "double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf.", "age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected", "GSM3855047", "GSM3855047: Wt DP R1med rep2; Danio rerio; RNA Seq", "GSM3855047", null, "1", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "GEO Accession:GSM3855047", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP200560", null, null, "WTCHG_236897_250_1_pair.fq.gz WTCHG_236897_250_2_pair.fq.gz", "fastq fastq", 2081468598.0, 14169082.0, "GSM3855047 r2", "0:74.83 1:72.07", "A:532025059;C:484883611;G:503099767;T:561423564;N:36597", 74, 72, null, null, 532025059, 484883611, 503099767, 561423564, 36597, "SRX5978255", "SRS4884510", "SRA894667", "GEO", "Oxford University", 2, 0.95742, 0.74712, 0.04275, 0.03741, 0.79922, 0.82866, 0.40398, 0.46313, 74, 74, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-06-05", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [52786, "SRR9207177", "SRX5978254", "SRS4884509", "SRP200560", "PRJNA547066", "RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf", "GSE132259", "Transcriptome Analysis", "The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.", "parent bioproject:PRJNA546805", "pubmed:31395869", null, "RNA seq Wt DP R1med rep1", "GSM3855046", null, "source name:aortic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected", "RNA seq Wt DP R1med rep1", "Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value.", "aortic endothelium", "double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf.", "age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected", "GSM3855046", "GSM3855046: Wt DP R1med rep1; Danio rerio; RNA Seq", "GSM3855046", null, "1", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "GEO Accession:GSM3855046", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP200560", null, null, "WTCHG_236896_243_1_pair.fq.gz WTCHG_236896_243_2_pair.fq.gz", "fastq fastq", 2011950216.0, 13680917.0, "GSM3855046 r1", "0:74.86 1:72.20", "A:511635564;C:476475475;G:489688294;T:534119393;N:31490", 74, 72, null, null, 511635564, 476475475, 489688294, 534119393, 31490, "SRX5978254", "SRS4884509", "SRA894667", "GEO", "Oxford University", 2, 0.9571, 0.78471, 0.03658, 0.03396, 0.80247, 0.8268, 0.48025, 0.46265, 74, 74, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-06-05", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [52787, "SRR9207178", "SRX5978254", "SRS4884509", "SRP200560", "PRJNA547066", "RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf", "GSE132259", "Transcriptome Analysis", "The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.", "parent bioproject:PRJNA546805", "pubmed:31395869", null, "RNA seq Wt DP R1med rep1", "GSM3855046", null, "source name:aortic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected", "RNA seq Wt DP R1med rep1", "Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value.", "aortic endothelium", "double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf.", "age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected", "GSM3855046", "GSM3855046: Wt DP R1med rep1; Danio rerio; RNA Seq", "GSM3855046", null, "1", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "GEO Accession:GSM3855046", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP200560", null, null, "WTCHG_236897_243_1_pair.fq.gz WTCHG_236897_243_2_pair.fq.gz", "fastq fastq", 1979368927.0, 13461179.0, "GSM3855046 r2", "0:74.83 1:72.21", "A:503539205;C:467446638;G:480794441;T:527553577;N:35066", 74, 72, null, null, 503539205, 467446638, 480794441, 527553577, 35066, "SRX5978254", "SRS4884509", "SRA894667", "GEO", "Oxford University", 2, 0.95558, 0.78357, 0.03711, 0.03412, 0.80318, 0.82664, 0.42185, 0.46216, 74, 64, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-06-05", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [52788, "SRR9207175", "SRX5978253", "SRS4884508", "SRP200560", "PRJNA547066", "RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf", "GSE132259", "Transcriptome Analysis", "The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.", "parent bioproject:PRJNA546805", "pubmed:31395869", null, "RNA seq Wt DP R1lo rep3", "GSM3855045", null, "source name:aortic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected", "RNA seq Wt DP R1lo rep3", "Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value.", "aortic endothelium", "double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf.", "age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected", "GSM3855045", "GSM3855045: Wt DP R1lo rep3; Danio rerio; RNA Seq", "GSM3855045", null, "1", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "GEO Accession:GSM3855045", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP200560", null, null, "WTCHG_236896_266_1_pair.fq.gz WTCHG_236896_266_2_pair.fq.gz", "fastq fastq", 2022090059.0, 13752247.0, "GSM3855045 r1", "0:74.84 1:72.20", "A:529671943;C:466470156;G:476864148;T:549051395;N:32417", 74, 72, null, null, 529671943, 466470156, 476864148, 549051395, 32417, "SRX5978253", "SRS4884508", "SRA894667", "GEO", "Oxford University", 2, 0.94638, 0.80375, 0.07924, 0.06889, 0.76098, 0.78636, 0.4888, 0.46168, 74, 74, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-06-05", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [52789, "SRR9207176", "SRX5978253", "SRS4884508", "SRP200560", "PRJNA547066", "RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf", "GSE132259", "Transcriptome Analysis", "The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.", "parent bioproject:PRJNA546805", "pubmed:31395869", null, "RNA seq Wt DP R1lo rep3", "GSM3855045", null, "source name:aortic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected", "RNA seq Wt DP R1lo rep3", "Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value.", "aortic endothelium", "double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf.", "age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected", "GSM3855045", "GSM3855045: Wt DP R1lo rep3; Danio rerio; RNA Seq", "GSM3855045", null, "1", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "GEO Accession:GSM3855045", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP200560", null, null, "WTCHG_236897_266_1_pair.fq.gz WTCHG_236897_266_2_pair.fq.gz", "fastq fastq", 1996491732.0, 13581226.0, "GSM3855045 r2", "0:74.81 1:72.20", "A:522970179;C:458424995;G:469211257;T:545848558;N:36743", 74, 72, null, null, 522970179, 458424995, 469211257, 545848558, 36743, "SRX5978253", "SRS4884508", "SRA894667", "GEO", "Oxford University", 2, 0.94571, 0.7947, 0.08062, 0.06773, 0.76116, 0.78591, 0.49549, 0.46742, 74, 74, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-06-05", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [52790, "SRR9207173", "SRX5978252", "SRS4884507", "SRP200560", "PRJNA547066", "RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf", "GSE132259", "Transcriptome Analysis", "The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.", "parent bioproject:PRJNA546805", "pubmed:31395869", null, "RNA seq Wt DP R1lo rep2", "GSM3855044", null, "source name:aortic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected", "RNA seq Wt DP R1lo rep2", "Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value.", "aortic endothelium", "double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf.", "age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected", "GSM3855044", "GSM3855044: Wt DP R1lo rep2; Danio rerio; RNA Seq", "GSM3855044", null, "1", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "GEO Accession:GSM3855044", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP200560", null, null, "WTCHG_236896_251_1_pair.fq.gz WTCHG_236896_251_2_pair.fq.gz", "fastq fastq", 2166575163.0, 14709523.0, "GSM3855044 r1", "0:74.86 1:72.43", "A:559933570;C:510454967;G:520888591;T:575264053;N:33982", 74, 72, null, null, 559933570, 510454967, 520888591, 575264053, 33982, "SRX5978252", "SRS4884507", "SRA894667", "GEO", "Oxford University", 2, 0.95094, 0.8211, 0.0594, 0.05292, 0.76664, 0.79253, 0.4795, 0.4638, 74, 74, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-06-05", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [52791, "SRR9207174", "SRX5978252", "SRS4884507", "SRP200560", "PRJNA547066", "RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf", "GSE132259", "Transcriptome Analysis", "The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.", "parent bioproject:PRJNA546805", "pubmed:31395869", null, "RNA seq Wt DP R1lo rep2", "GSM3855044", null, "source name:aortic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected", "RNA seq Wt DP R1lo rep2", "Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value.", "aortic endothelium", "double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf.", "age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected", "GSM3855044", "GSM3855044: Wt DP R1lo rep2; Danio rerio; RNA Seq", "GSM3855044", null, "1", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "GEO Accession:GSM3855044", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP200560", null, null, "WTCHG_236897_251_1_pair.fq.gz WTCHG_236897_251_2_pair.fq.gz", "fastq fastq", 2148630324.0, 14593830.0, "GSM3855044 r2", "0:74.83 1:72.40", "A:555362600;C:503529612;G:514542689;T:575156489;N:38934", 74, 72, null, null, 555362600, 503529612, 514542689, 575156489, 38934, "SRX5978252", "SRS4884507", "SRA894667", "GEO", "Oxford University", 2, 0.95053, 0.81036, 0.06102, 0.05199, 0.76897, 0.79354, 0.47523, 0.46186, 74, 74, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-06-05", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [52792, "SRR9207171", "SRX5978251", "SRS4884506", "SRP200560", "PRJNA547066", "RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf", "GSE132259", "Transcriptome Analysis", "The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.", "parent bioproject:PRJNA546805", "pubmed:31395869", null, "RNA seq Wt DP R1lo rep1", "GSM3855043", null, "source name:aortic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected", "RNA seq Wt DP R1lo rep1", "Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value.", "aortic endothelium", "double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf.", "age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected", "GSM3855043", "GSM3855043: Wt DP R1lo rep1; Danio rerio; RNA Seq", "GSM3855043", null, "1", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "GEO Accession:GSM3855043", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP200560", null, null, "WTCHG_236896_244_1_pair.fq.gz WTCHG_236896_244_2_pair.fq.gz", "fastq fastq", 1899807957.0, 12921335.0, "GSM3855043 r1", "0:74.85 1:72.17", "A:494455972;C:440267035;G:451386907;T:513668319;N:29724", 74, 72, null, null, 494455972, 440267035, 451386907, 513668319, 29724, "SRX5978251", "SRS4884506", "SRA894667", "GEO", "Oxford University", 2, 0.94888, 0.79567, 0.06354, 0.05518, 0.77041, 0.79837, 0.48973, 0.47834, 75, 73, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "full_length", "cdna_unspecified", "smarter", "bulk", "unknown", "unknown", null, "United Kingdom", "2019-06-05", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [52793, "SRR9207172", "SRX5978251", "SRS4884506", "SRP200560", "PRJNA547066", "RNAseq of haemogenic and aortic endothelium in zebrafish embryos 28 hpf 20 hpf", "GSE132259", "Transcriptome Analysis", "The goal of this study is to perform RNAseq in different sub types of the zebrafish embryonic dorsal aorta DA at 28 hpf 30 hpf using TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.", "parent bioproject:PRJNA546805", "pubmed:31395869", null, "RNA seq Wt DP R1lo rep1", "GSM3855043", null, "source name:aortic endothelium|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected", "RNA seq Wt DP R1lo rep1", "Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value.", "aortic endothelium", "double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf.", "age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:aortic endothelium|genotype/variation:non injected", "GSM3855043", "GSM3855043: Wt DP R1lo rep1; Danio rerio; RNA Seq", "GSM3855043", null, "1", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. 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A min. of 3000 cells per population were collected via FACS. RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used to generate SMARTer libraries for low input RNA. Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. Overall design: Analysis of 5 different cell types; DN double negative SP kdrl single positive DP R1lo double positive runx1 low expression DP R1med runx1 medium expressionand and DP R1hi runx1 high expression in non injected Wt TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos. Analysis was also done of the DN and DP R1hi populations in runx1 morpholino MO injected embryos.", "parent bioproject:PRJNA546805", "pubmed:31395869", null, "RNA seq Wt DN rep3", "GSM3855039", null, "source name:non endothelial tissue|age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:non injected", "RNA seq Wt DN rep3", "Sequencing was performed on an Illumina HiSeq4000 machine with a 75 bp paired end protocol. Sequenced reads were checked for base qualities trimmed where 20% of the bases were below quality score 20 and filtered to exclude adapters using Trimmomatic Version 0.32. Sequences were aligned to the Zebrafish Genome Zv10 with STAR with default parameters. Aligned read features were counted using Subread tool: featureCounts method version 1.4.5 p1. To determine number of mapped reads we used the trimmed data. The alignment has been performed using STAR with default parameters. The number of mapped reads QC passed reads count has been obtain using Samtools mapping statistics flagstat tool. RAW data files represent the trimmed sequencing reads in separated lanes. Genome build: Zv10 Supplementary files format and content: Wt DP R1hi Wt DP R1lo Differential analysis between Wt DP R1hi and Wt DP R1lo cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DP R1hi MO DP R1hi Differential analysis between Wt DP R1hi and MO DP R1hi cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value. Supplementary files format and content: Wt DN MO DN Differential analysis between Wt DN and MO DN cell type. The xlsx file contains edgeR normalisation and GLM estimation of dispersion. The file contains gene id Counts Per Million gene name end value of each sample log FC wt/mo P value and FDR value.", "non endothelial tissue", "double transgenic embryos were collected batches were split in half and were either injected or non injected with a runx1 morpholino", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. High quality RNA RIN > 8.0 was sent for RNAseq to the Wellcome Trust Centre for Human Genetics WTCHG. 2.2 ng of total RNA was used for to generate SMARTer libraries for low input RNA.", "TgBACrunx1P2:Citrine;Tgkdrl:mCherry double transgenic zebrafish embryos were raised to 28 hpf 30 hpf.", "age:28 hpf 30 hpf|cell isolation:FACS isolated cells|tissue:non endothelial tissue|genotype/variation:non injected", "GSM3855039", "GSM3855039: Wt DN rep3; Danio rerio; RNA Seq", "GSM3855039", null, "1", "whole embryos were prepaired for FACsorting. A min. of 3000 cells were FACsorted directly into RLT buffer and RNA was isolated with the RNeasy Plus Micro Kit QIAGEN Cat No. 74034. 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