{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"PAIRED\", technology = \"smartseq\" and tissue_curation = \"Endothelium\"", "rows": [[58567, "SRR11420478", "SRX7998914", "SRS6376277", "SRP254020", "PRJNA615175", "A Zebrafish Based Orthotopic Glioblastoma Xenograft Model for Preclinical Drug Screening and Clinical Drug Sensitivity Prediction", "GSE147526", "Other", "A reliable animal model that can mimic the GBM intracranial infiltration and Blood brain barrier BBB interaction is necessary for effective therapeutics development. Here  we report a zebrafish based orthotopic GBM xenograft model  in which GBM cells from different species and even patients  can robustly propagate and faithfully reproduce their histological characteristics. Single cell RNA seq indicates a transcriptomic adaption of GBM xenografts to infiltrative phenotype within the zebrafish brains. We also provide evidence that the BBB in zebrafish larva is molecularly and functionally intact and can interact with GBM cells in similar ways as in mammals  which together enables this model to accurately identify BBB penetrating drugs. Using GBM patients' samples  we further generate zebrafish patient derived orthotopic xenografts z PDOX and proof of concept experiments indicate the short term temozolomide response in z PDOX can predict the long term prognosis of corresponding GBM patients. These together illustrate the value of zebrafish GBM model in drug discovery and precision medicine. Overall design: 1.Single cell RNA seq for endothelial cells of zebrafish 2.Single cell RNA seq for GBM cells implanted in zebrafish brain", null, "pubmed:35199829", null, "Smartseq2 AXL E3 endo Danio", "GSM4432625", null, "tissue:endothelial cells|strain:flk:GFP|cell tye:endothelial cells", "Smartseq2 AXL E3 endo Danio", "ScRNA seq alignment process was completed by STAR 2.6.0a DESeq2 standard workflow Genome build: GRCz10 genome references for Zebrafish and GRCh38 genome references for human Supplementary files format and content: csv files with raw counts and FPKM", "endothelial cells", null, "1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope  the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope  a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle.   2. For GBM cells  zebrafish were injected with GBM U251 mCherry cells  and allowed to form widespread  tumor invasion for xxx 5 days. At that point  the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope  the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously  GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the 3\u2019 scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang  2010.", null, "strain:flk:GFP|cell tye:endothelial cells", "GSM4432625", "GSM4432625: Smartseq2 AXL E3 endo Danio; Danio rerio; RNA Seq", "GSM4432625", null, "1", "1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope  the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope  a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle.   2. For GBM cells  zebrafish were injected with GBM U251 mCherry cells  and allowed to form widespread  tumor invasion for xxx 5 days. At that point  the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope  the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously  GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. 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Here  we report a zebrafish based orthotopic GBM xenograft model  in which GBM cells from different species and even patients  can robustly propagate and faithfully reproduce their histological characteristics. Single cell RNA seq indicates a transcriptomic adaption of GBM xenografts to infiltrative phenotype within the zebrafish brains. We also provide evidence that the BBB in zebrafish larva is molecularly and functionally intact and can interact with GBM cells in similar ways as in mammals  which together enables this model to accurately identify BBB penetrating drugs. Using GBM patients' samples  we further generate zebrafish patient derived orthotopic xenografts z PDOX and proof of concept experiments indicate the short term temozolomide response in z PDOX can predict the long term prognosis of corresponding GBM patients. These together illustrate the value of zebrafish GBM model in drug discovery and precision medicine. Overall design: 1.Single cell RNA seq for endothelial cells of zebrafish 2.Single cell RNA seq for GBM cells implanted in zebrafish brain", null, "pubmed:35199829", null, "Smartseq2 AXL E2 endo Danio", "GSM4432624", null, "tissue:endothelial cells|strain:flk:GFP|cell tye:endothelial cells", "Smartseq2 AXL E2 endo Danio", "ScRNA seq alignment process was completed by STAR 2.6.0a DESeq2 standard workflow Genome build: GRCz10 genome references for Zebrafish and GRCh38 genome references for human Supplementary files format and content: csv files with raw counts and FPKM", "endothelial cells", null, "1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope  the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope  a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle.   2. For GBM cells  zebrafish were injected with GBM U251 mCherry cells  and allowed to form widespread  tumor invasion for xxx 5 days. At that point  the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope  the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously  GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the 3\u2019 scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang  2010.", null, "strain:flk:GFP|cell tye:endothelial cells", "GSM4432624", "GSM4432624: Smartseq2 AXL E2 endo Danio; Danio rerio; RNA Seq", "GSM4432624", null, "1", "1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope  the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope  a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle.   2. For GBM cells  zebrafish were injected with GBM U251 mCherry cells  and allowed to form widespread  tumor invasion for xxx 5 days. At that point  the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope  the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously  GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. 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Here  we report a zebrafish based orthotopic GBM xenograft model  in which GBM cells from different species and even patients  can robustly propagate and faithfully reproduce their histological characteristics. Single cell RNA seq indicates a transcriptomic adaption of GBM xenografts to infiltrative phenotype within the zebrafish brains. We also provide evidence that the BBB in zebrafish larva is molecularly and functionally intact and can interact with GBM cells in similar ways as in mammals  which together enables this model to accurately identify BBB penetrating drugs. Using GBM patients' samples  we further generate zebrafish patient derived orthotopic xenografts z PDOX and proof of concept experiments indicate the short term temozolomide response in z PDOX can predict the long term prognosis of corresponding GBM patients. These together illustrate the value of zebrafish GBM model in drug discovery and precision medicine. Overall design: 1.Single cell RNA seq for endothelial cells of zebrafish 2.Single cell RNA seq for GBM cells implanted in zebrafish brain", null, "pubmed:35199829", null, "Smartseq2 AXL E1 endo Danio", "GSM4432623", null, "tissue:endothelial cells|strain:flk:GFP|cell tye:endothelial cells", "Smartseq2 AXL E1 endo Danio", "ScRNA seq alignment process was completed by STAR 2.6.0a DESeq2 standard workflow Genome build: GRCz10 genome references for Zebrafish and GRCh38 genome references for human Supplementary files format and content: csv files with raw counts and FPKM", "endothelial cells", null, "1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope  the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope  a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle.   2. For GBM cells  zebrafish were injected with GBM U251 mCherry cells  and allowed to form widespread  tumor invasion for xxx 5 days. At that point  the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope  the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously  GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the 3\u2019 scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang  2010.", null, "strain:flk:GFP|cell tye:endothelial cells", "GSM4432623", "GSM4432623: Smartseq2 AXL E1 endo Danio; Danio rerio; RNA Seq", "GSM4432623", null, "1", "1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope  the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope  a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle.   2. For GBM cells  zebrafish were injected with GBM U251 mCherry cells  and allowed to form widespread  tumor invasion for xxx 5 days. At that point  the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope  the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously  GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. 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Here  we report a zebrafish based orthotopic GBM xenograft model  in which GBM cells from different species and even patients  can robustly propagate and faithfully reproduce their histological characteristics. Single cell RNA seq indicates a transcriptomic adaption of GBM xenografts to infiltrative phenotype within the zebrafish brains. We also provide evidence that the BBB in zebrafish larva is molecularly and functionally intact and can interact with GBM cells in similar ways as in mammals  which together enables this model to accurately identify BBB penetrating drugs. Using GBM patients' samples  we further generate zebrafish patient derived orthotopic xenografts z PDOX and proof of concept experiments indicate the short term temozolomide response in z PDOX can predict the long term prognosis of corresponding GBM patients. These together illustrate the value of zebrafish GBM model in drug discovery and precision medicine. Overall design: 1.Single cell RNA seq for endothelial cells of zebrafish 2.Single cell RNA seq for GBM cells implanted in zebrafish brain", null, "pubmed:35199829", null, "Smartseq2 AXL D3 endo Danio", "GSM4432622", null, "tissue:endothelial cells|strain:flk:GFP|cell tye:endothelial cells", "Smartseq2 AXL D3 endo Danio", "ScRNA seq alignment process was completed by STAR 2.6.0a DESeq2 standard workflow Genome build: GRCz10 genome references for Zebrafish and GRCh38 genome references for human Supplementary files format and content: csv files with raw counts and FPKM", "endothelial cells", null, "1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope  the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope  a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle.   2. For GBM cells  zebrafish were injected with GBM U251 mCherry cells  and allowed to form widespread  tumor invasion for xxx 5 days. At that point  the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope  the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously  GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the 3\u2019 scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang  2010.", null, "strain:flk:GFP|cell tye:endothelial cells", "GSM4432622", "GSM4432622: Smartseq2 AXL D3 endo Danio; Danio rerio; RNA Seq", "GSM4432622", null, "1", "1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope  the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope  a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle.   2. For GBM cells  zebrafish were injected with GBM U251 mCherry cells  and allowed to form widespread  tumor invasion for xxx 5 days. At that point  the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope  the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously  GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. 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Here  we report a zebrafish based orthotopic GBM xenograft model  in which GBM cells from different species and even patients  can robustly propagate and faithfully reproduce their histological characteristics. Single cell RNA seq indicates a transcriptomic adaption of GBM xenografts to infiltrative phenotype within the zebrafish brains. We also provide evidence that the BBB in zebrafish larva is molecularly and functionally intact and can interact with GBM cells in similar ways as in mammals  which together enables this model to accurately identify BBB penetrating drugs. Using GBM patients' samples  we further generate zebrafish patient derived orthotopic xenografts z PDOX and proof of concept experiments indicate the short term temozolomide response in z PDOX can predict the long term prognosis of corresponding GBM patients. These together illustrate the value of zebrafish GBM model in drug discovery and precision medicine. Overall design: 1.Single cell RNA seq for endothelial cells of zebrafish 2.Single cell RNA seq for GBM cells implanted in zebrafish brain", null, "pubmed:35199829", null, "Smartseq2 AXL C3 endo Danio", "GSM4432621", null, "tissue:endothelial cells|strain:flk:GFP|cell tye:endothelial cells", "Smartseq2 AXL C3 endo Danio", "ScRNA seq alignment process was completed by STAR 2.6.0a DESeq2 standard workflow Genome build: GRCz10 genome references for Zebrafish and GRCh38 genome references for human Supplementary files format and content: csv files with raw counts and FPKM", "endothelial cells", null, "1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope  the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope  a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle.   2. For GBM cells  zebrafish were injected with GBM U251 mCherry cells  and allowed to form widespread  tumor invasion for xxx 5 days. At that point  the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope  the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously  GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the 3\u2019 scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang  2010.", null, "strain:flk:GFP|cell tye:endothelial cells", "GSM4432621", "GSM4432621: Smartseq2 AXL C3 endo Danio; Danio rerio; RNA Seq", "GSM4432621", null, "1", "1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope  the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope  a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle.   2. For GBM cells  zebrafish were injected with GBM U251 mCherry cells  and allowed to form widespread  tumor invasion for xxx 5 days. At that point  the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope  the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously  GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the three prime scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang  2010.", "GEO Accession:GSM4432621", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP254020", null, null, "AXL-C3_HHVK7CCXY_L3_1.clean.fq.gz AXL-C3_HHVK7CCXY_L3_2.clean.fq.gz", "fastq fastq", 1574724600.0, 5249082.0, "GSM4432621 r1", "0:150 1:150", "A:435586693;C:313192449;G:325059370;T:500799470;N:86618", 150, 150, null, null, 435586693, 313192449, 325059370, 500799470, 86618, "SRX7998910", "SRS6376273", "SRA1059261", "GEO", "Chen & Liu Lab, State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University., Sichuan University", 2, 0.91247, 0.91968, 0.66959, 0.67559, 0.94515, 0.94734, 0.47277, 0.49142, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2020-03-25", "Larval", "Larval", "Endothelium", "Cardiovascular System"], [58572, "SRR11420473", "SRX7998909", "SRS6376272", "SRP254020", "PRJNA615175", "A Zebrafish Based Orthotopic Glioblastoma Xenograft Model for Preclinical Drug Screening and Clinical Drug Sensitivity Prediction", "GSE147526", "Other", "A reliable animal model that can mimic the GBM intracranial infiltration and Blood brain barrier BBB interaction is necessary for effective therapeutics development. Here  we report a zebrafish based orthotopic GBM xenograft model  in which GBM cells from different species and even patients  can robustly propagate and faithfully reproduce their histological characteristics. Single cell RNA seq indicates a transcriptomic adaption of GBM xenografts to infiltrative phenotype within the zebrafish brains. We also provide evidence that the BBB in zebrafish larva is molecularly and functionally intact and can interact with GBM cells in similar ways as in mammals  which together enables this model to accurately identify BBB penetrating drugs. Using GBM patients' samples  we further generate zebrafish patient derived orthotopic xenografts z PDOX and proof of concept experiments indicate the short term temozolomide response in z PDOX can predict the long term prognosis of corresponding GBM patients. These together illustrate the value of zebrafish GBM model in drug discovery and precision medicine. Overall design: 1.Single cell RNA seq for endothelial cells of zebrafish 2.Single cell RNA seq for GBM cells implanted in zebrafish brain", null, "pubmed:35199829", null, "Smartseq2 AXL C2 endo Danio", "GSM4432620", null, "tissue:endothelial cells|strain:flk:GFP|cell tye:endothelial cells", "Smartseq2 AXL C2 endo Danio", "ScRNA seq alignment process was completed by STAR 2.6.0a DESeq2 standard workflow Genome build: GRCz10 genome references for Zebrafish and GRCh38 genome references for human Supplementary files format and content: csv files with raw counts and FPKM", "endothelial cells", null, "1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope  the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope  a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle.   2. For GBM cells  zebrafish were injected with GBM U251 mCherry cells  and allowed to form widespread  tumor invasion for xxx 5 days. At that point  the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope  the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously  GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the 3\u2019 scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang  2010.", null, "strain:flk:GFP|cell tye:endothelial cells", "GSM4432620", "GSM4432620: Smartseq2 AXL C2 endo Danio; Danio rerio; RNA Seq", "GSM4432620", null, "1", "1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope  the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope  a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle.   2. For GBM cells  zebrafish were injected with GBM U251 mCherry cells  and allowed to form widespread  tumor invasion for xxx 5 days. At that point  the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope  the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously  GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the three prime scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang  2010.", "GEO Accession:GSM4432620", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP254020", null, null, "AXL-C2_HHVK7CCXY_L3_1.clean.fq.gz AXL-C2_HHVK7CCXY_L3_2.clean.fq.gz", "fastq fastq", 918029400.0, 3060098.0, "GSM4432620 r1", "0:150 1:150", "A:247708437;C:197427436;G:203244315;T:269598842;N:50370", 150, 150, null, null, 247708437, 197427436, 203244315, 269598842, 50370, "SRX7998909", "SRS6376272", "SRA1059261", "GEO", "Chen & Liu Lab, State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University., Sichuan University", 2, 0.85585, 0.86096, 0.18376, 0.1852, 0.91352, 0.91571, 0.44329, 0.55709, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2020-03-25", "Larval", "Larval", "Endothelium", "Cardiovascular System"], [58573, "SRR11420472", "SRX7998908", "SRS6376270", "SRP254020", "PRJNA615175", "A Zebrafish Based Orthotopic Glioblastoma Xenograft Model for Preclinical Drug Screening and Clinical Drug Sensitivity Prediction", "GSE147526", "Other", "A reliable animal model that can mimic the GBM intracranial infiltration and Blood brain barrier BBB interaction is necessary for effective therapeutics development. Here  we report a zebrafish based orthotopic GBM xenograft model  in which GBM cells from different species and even patients  can robustly propagate and faithfully reproduce their histological characteristics. Single cell RNA seq indicates a transcriptomic adaption of GBM xenografts to infiltrative phenotype within the zebrafish brains. We also provide evidence that the BBB in zebrafish larva is molecularly and functionally intact and can interact with GBM cells in similar ways as in mammals  which together enables this model to accurately identify BBB penetrating drugs. Using GBM patients' samples  we further generate zebrafish patient derived orthotopic xenografts z PDOX and proof of concept experiments indicate the short term temozolomide response in z PDOX can predict the long term prognosis of corresponding GBM patients. These together illustrate the value of zebrafish GBM model in drug discovery and precision medicine. Overall design: 1.Single cell RNA seq for endothelial cells of zebrafish 2.Single cell RNA seq for GBM cells implanted in zebrafish brain", null, "pubmed:35199829", null, "Smartseq2 AXL C1 endo Danio", "GSM4432619", null, "tissue:endothelial cells|strain:flk:GFP|cell tye:endothelial cells", "Smartseq2 AXL C1 endo Danio", "ScRNA seq alignment process was completed by STAR 2.6.0a DESeq2 standard workflow Genome build: GRCz10 genome references for Zebrafish and GRCh38 genome references for human Supplementary files format and content: csv files with raw counts and FPKM", "endothelial cells", null, "1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope  the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope  a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle.   2. For GBM cells  zebrafish were injected with GBM U251 mCherry cells  and allowed to form widespread  tumor invasion for xxx 5 days. At that point  the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope  the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously  GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the 3\u2019 scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang  2010.", null, "strain:flk:GFP|cell tye:endothelial cells", "GSM4432619", "GSM4432619: Smartseq2 AXL C1 endo Danio; Danio rerio; RNA Seq", "GSM4432619", null, "1", "1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope  the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope  a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle.   2. For GBM cells  zebrafish were injected with GBM U251 mCherry cells  and allowed to form widespread  tumor invasion for xxx 5 days. At that point  the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope  the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously  GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the three prime scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang  2010.", "GEO Accession:GSM4432619", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP254020", null, null, "AXL-C1_HHVK7CCXY_L3_1.clean.fq.gz AXL-C1_HHVK7CCXY_L3_2.clean.fq.gz", "fastq fastq", 1500775500.0, 5002585.0, "GSM4432619 r1", "0:150 1:150", "A:432671655;C:289434226;G:302125698;T:476460891;N:83030", 150, 150, null, null, 432671655, 289434226, 302125698, 476460891, 83030, "SRX7998908", "SRS6376270", "SRA1059261", "GEO", "Chen & Liu Lab, State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University., Sichuan University", 2, 0.67663, 0.68022, 0.32993, 0.33204, 0.86841, 0.87373, 0.55098, 0.55286, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2020-03-25", "Larval", "Larval", "Endothelium", "Cardiovascular System"], [58574, "SRR11420471", "SRX7998907", "SRS6376271", "SRP254020", "PRJNA615175", "A Zebrafish Based Orthotopic Glioblastoma Xenograft Model for Preclinical Drug Screening and Clinical Drug Sensitivity Prediction", "GSE147526", "Other", "A reliable animal model that can mimic the GBM intracranial infiltration and Blood brain barrier BBB interaction is necessary for effective therapeutics development. Here  we report a zebrafish based orthotopic GBM xenograft model  in which GBM cells from different species and even patients  can robustly propagate and faithfully reproduce their histological characteristics. Single cell RNA seq indicates a transcriptomic adaption of GBM xenografts to infiltrative phenotype within the zebrafish brains. We also provide evidence that the BBB in zebrafish larva is molecularly and functionally intact and can interact with GBM cells in similar ways as in mammals  which together enables this model to accurately identify BBB penetrating drugs. Using GBM patients' samples  we further generate zebrafish patient derived orthotopic xenografts z PDOX and proof of concept experiments indicate the short term temozolomide response in z PDOX can predict the long term prognosis of corresponding GBM patients. These together illustrate the value of zebrafish GBM model in drug discovery and precision medicine. Overall design: 1.Single cell RNA seq for endothelial cells of zebrafish 2.Single cell RNA seq for GBM cells implanted in zebrafish brain", null, "pubmed:35199829", null, "Smartseq2 AXL B2 endo Danio", "GSM4432618", null, "tissue:endothelial cells|strain:flk:GFP|cell tye:endothelial cells", "Smartseq2 AXL B2 endo Danio", "ScRNA seq alignment process was completed by STAR 2.6.0a DESeq2 standard workflow Genome build: GRCz10 genome references for Zebrafish and GRCh38 genome references for human Supplementary files format and content: csv files with raw counts and FPKM", "endothelial cells", null, "1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope  the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope  a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle.   2. For GBM cells  zebrafish were injected with GBM U251 mCherry cells  and allowed to form widespread  tumor invasion for xxx 5 days. At that point  the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope  the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously  GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the 3\u2019 scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang  2010.", null, "strain:flk:GFP|cell tye:endothelial cells", "GSM4432618", "GSM4432618: Smartseq2 AXL B2 endo Danio; Danio rerio; RNA Seq", "GSM4432618", null, "1", "1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope  the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope  a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle.   2. For GBM cells  zebrafish were injected with GBM U251 mCherry cells  and allowed to form widespread  tumor invasion for xxx 5 days. At that point  the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope  the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously  GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the three prime scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang  2010.", "GEO Accession:GSM4432618", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP254020", null, null, "AXL-B2_HHVK7CCXY_L3_1.clean.fq.gz AXL-B2_HHVK7CCXY_L3_2.clean.fq.gz", "fastq fastq", 989060100.0, 3296867.0, "GSM4432618 r1", "0:150 1:150", "A:274301021;C:196555336;G:203736274;T:314412137;N:55332", 150, 150, null, null, 274301021, 196555336, 203736274, 314412137, 55332, "SRX7998907", "SRS6376271", "SRA1059261", "GEO", "Chen & Liu Lab, State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University., Sichuan University", 2, 0.9149, 0.92243, 0.73373, 0.73884, 0.95296, 0.95426, 0.47934, 0.47668, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2020-03-25", "Larval", "Larval", "Endothelium", "Cardiovascular System"], [58575, "SRR11420470", "SRX7998906", "SRS6376269", "SRP254020", "PRJNA615175", "A Zebrafish Based Orthotopic Glioblastoma Xenograft Model for Preclinical Drug Screening and Clinical Drug Sensitivity Prediction", "GSE147526", "Other", "A reliable animal model that can mimic the GBM intracranial infiltration and Blood brain barrier BBB interaction is necessary for effective therapeutics development. Here  we report a zebrafish based orthotopic GBM xenograft model  in which GBM cells from different species and even patients  can robustly propagate and faithfully reproduce their histological characteristics. Single cell RNA seq indicates a transcriptomic adaption of GBM xenografts to infiltrative phenotype within the zebrafish brains. We also provide evidence that the BBB in zebrafish larva is molecularly and functionally intact and can interact with GBM cells in similar ways as in mammals  which together enables this model to accurately identify BBB penetrating drugs. Using GBM patients' samples  we further generate zebrafish patient derived orthotopic xenografts z PDOX and proof of concept experiments indicate the short term temozolomide response in z PDOX can predict the long term prognosis of corresponding GBM patients. These together illustrate the value of zebrafish GBM model in drug discovery and precision medicine. Overall design: 1.Single cell RNA seq for endothelial cells of zebrafish 2.Single cell RNA seq for GBM cells implanted in zebrafish brain", null, "pubmed:35199829", null, "Smartseq2 AXL B1 endo Danio", "GSM4432617", null, "tissue:endothelial cells|strain:flk:GFP|cell tye:endothelial cells", "Smartseq2 AXL B1 endo Danio", "ScRNA seq alignment process was completed by STAR 2.6.0a DESeq2 standard workflow Genome build: GRCz10 genome references for Zebrafish and GRCh38 genome references for human Supplementary files format and content: csv files with raw counts and FPKM", "endothelial cells", null, "1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope  the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope  a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle.   2. For GBM cells  zebrafish were injected with GBM U251 mCherry cells  and allowed to form widespread  tumor invasion for xxx 5 days. At that point  the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope  the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously  GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the 3\u2019 scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang  2010.", null, "strain:flk:GFP|cell tye:endothelial cells", "GSM4432617", "GSM4432617: Smartseq2 AXL B1 endo Danio; Danio rerio; RNA Seq", "GSM4432617", null, "1", "1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope  the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope  a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle.   2. For GBM cells  zebrafish were injected with GBM U251 mCherry cells  and allowed to form widespread  tumor invasion for xxx 5 days. At that point  the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope  the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously  GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the three prime scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang  2010.", "GEO Accession:GSM4432617", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP254020", null, null, "AXL-B1_HHVK7CCXY_L3_1.clean.fq.gz AXL-B1_HHVK7CCXY_L3_2.clean.fq.gz", "fastq fastq", 2099031600.0, 6996772.0, "GSM4432617 r1", "0:150 1:150", "A:583452672;C:414863616;G:430728068;T:669871636;N:115608", 150, 150, null, null, 583452672, 414863616, 430728068, 669871636, 115608, "SRX7998906", "SRS6376269", "SRA1059261", "GEO", "Chen & Liu Lab, State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University., Sichuan University", 2, 0.82207, 0.82952, 0.63293, 0.64238, 0.94602, 0.94828, 0.49299, 0.49862, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2020-03-25", "Larval", "Larval", "Endothelium", "Cardiovascular System"], [58576, "SRR11420469", "SRX7998905", "SRS6376268", "SRP254020", "PRJNA615175", "A Zebrafish Based Orthotopic Glioblastoma Xenograft Model for Preclinical Drug Screening and Clinical Drug Sensitivity Prediction", "GSE147526", "Other", "A reliable animal model that can mimic the GBM intracranial infiltration and Blood brain barrier BBB interaction is necessary for effective therapeutics development. Here  we report a zebrafish based orthotopic GBM xenograft model  in which GBM cells from different species and even patients  can robustly propagate and faithfully reproduce their histological characteristics. Single cell RNA seq indicates a transcriptomic adaption of GBM xenografts to infiltrative phenotype within the zebrafish brains. We also provide evidence that the BBB in zebrafish larva is molecularly and functionally intact and can interact with GBM cells in similar ways as in mammals  which together enables this model to accurately identify BBB penetrating drugs. Using GBM patients' samples  we further generate zebrafish patient derived orthotopic xenografts z PDOX and proof of concept experiments indicate the short term temozolomide response in z PDOX can predict the long term prognosis of corresponding GBM patients. These together illustrate the value of zebrafish GBM model in drug discovery and precision medicine. Overall design: 1.Single cell RNA seq for endothelial cells of zebrafish 2.Single cell RNA seq for GBM cells implanted in zebrafish brain", null, "pubmed:35199829", null, "Smartseq2 AXL A3 endo Danio", "GSM4432616", null, "tissue:endothelial cells|strain:flk:GFP|cell tye:endothelial cells", "Smartseq2 AXL A3 endo Danio", "ScRNA seq alignment process was completed by STAR 2.6.0a DESeq2 standard workflow Genome build: GRCz10 genome references for Zebrafish and GRCh38 genome references for human Supplementary files format and content: csv files with raw counts and FPKM", "endothelial cells", null, "1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope  the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope  a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle.   2. For GBM cells  zebrafish were injected with GBM U251 mCherry cells  and allowed to form widespread  tumor invasion for xxx 5 days. At that point  the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope  the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously  GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the 3\u2019 scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang  2010.", null, "strain:flk:GFP|cell tye:endothelial cells", "GSM4432616", "GSM4432616: Smartseq2 AXL A3 endo Danio; Danio rerio; RNA Seq", "GSM4432616", null, "1", "1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope  the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope  a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle.   2. For GBM cells  zebrafish were injected with GBM U251 mCherry cells  and allowed to form widespread  tumor invasion for xxx 5 days. At that point  the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope  the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously  GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the three prime scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang  2010.", "GEO Accession:GSM4432616", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP254020", null, null, "AXL-A3_HHVK7CCXY_L3_1.clean.fq.gz AXL-A3_HHVK7CCXY_L3_2.clean.fq.gz", "fastq fastq", 932495100.0, 3108317.0, "GSM4432616 r1", "0:150 1:150", "A:258055487;C:185801372;G:192600723;T:295985361;N:52157", 150, 150, null, null, 258055487, 185801372, 192600723, 295985361, 52157, "SRX7998905", "SRS6376268", "SRA1059261", "GEO", "Chen & Liu Lab, State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University., Sichuan University", 2, 0.91666, 0.92212, 0.7484, 0.75372, 0.94826, 0.95018, 0.50494, 0.50846, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2020-03-25", "Larval", "Larval", "Endothelium", "Cardiovascular System"], [58577, "SRR11420468", "SRX7998904", "SRS6376267", "SRP254020", "PRJNA615175", "A Zebrafish Based Orthotopic Glioblastoma Xenograft Model for Preclinical Drug Screening and Clinical Drug Sensitivity Prediction", "GSE147526", "Other", "A reliable animal model that can mimic the GBM intracranial infiltration and Blood brain barrier BBB interaction is necessary for effective therapeutics development. Here  we report a zebrafish based orthotopic GBM xenograft model  in which GBM cells from different species and even patients  can robustly propagate and faithfully reproduce their histological characteristics. Single cell RNA seq indicates a transcriptomic adaption of GBM xenografts to infiltrative phenotype within the zebrafish brains. We also provide evidence that the BBB in zebrafish larva is molecularly and functionally intact and can interact with GBM cells in similar ways as in mammals  which together enables this model to accurately identify BBB penetrating drugs. Using GBM patients' samples  we further generate zebrafish patient derived orthotopic xenografts z PDOX and proof of concept experiments indicate the short term temozolomide response in z PDOX can predict the long term prognosis of corresponding GBM patients. These together illustrate the value of zebrafish GBM model in drug discovery and precision medicine. Overall design: 1.Single cell RNA seq for endothelial cells of zebrafish 2.Single cell RNA seq for GBM cells implanted in zebrafish brain", null, "pubmed:35199829", null, "Smartseq2 AXL A2 endo Danio", "GSM4432615", null, "tissue:endothelial cells|strain:flk:GFP|cell tye:endothelial cells", "Smartseq2 AXL A2 endo Danio", "ScRNA seq alignment process was completed by STAR 2.6.0a DESeq2 standard workflow Genome build: GRCz10 genome references for Zebrafish and GRCh38 genome references for human Supplementary files format and content: csv files with raw counts and FPKM", "endothelial cells", null, "1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope  the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope  a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle.   2. For GBM cells  zebrafish were injected with GBM U251 mCherry cells  and allowed to form widespread  tumor invasion for xxx 5 days. At that point  the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope  the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously  GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the 3\u2019 scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang  2010.", null, "strain:flk:GFP|cell tye:endothelial cells", "GSM4432615", "GSM4432615: Smartseq2 AXL A2 endo Danio; Danio rerio; RNA Seq", "GSM4432615", null, "1", "1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope  the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope  a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle.   2. For GBM cells  zebrafish were injected with GBM U251 mCherry cells  and allowed to form widespread  tumor invasion for xxx 5 days. At that point  the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope  the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously  GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the three prime scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang  2010.", "GEO Accession:GSM4432615", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP254020", null, null, "AXL-A2_HHVK7CCXY_L3_1.clean.fq.gz AXL-A2_HHVK7CCXY_L3_2.clean.fq.gz", "fastq fastq", 1474053600.0, 4913512.0, "GSM4432615 r1", "0:150 1:150", "A:409235463;C:294510014;G:304366926;T:465858337;N:82860", 150, 150, null, null, 409235463, 294510014, 304366926, 465858337, 82860, "SRX7998904", "SRS6376267", "SRA1059261", "GEO", "Chen & Liu Lab, State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University., Sichuan University", 2, 0.89481, 0.90098, 0.57187, 0.57596, 0.91045, 0.91366, 0.46573, 0.46566, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2020-03-25", "Larval", "Larval", "Endothelium", "Cardiovascular System"], [58578, "SRR11420467", "SRX7998903", "SRS6376266", "SRP254020", "PRJNA615175", "A Zebrafish Based Orthotopic Glioblastoma Xenograft Model for Preclinical Drug Screening and Clinical Drug Sensitivity Prediction", "GSE147526", "Other", "A reliable animal model that can mimic the GBM intracranial infiltration and Blood brain barrier BBB interaction is necessary for effective therapeutics development. Here  we report a zebrafish based orthotopic GBM xenograft model  in which GBM cells from different species and even patients  can robustly propagate and faithfully reproduce their histological characteristics. Single cell RNA seq indicates a transcriptomic adaption of GBM xenografts to infiltrative phenotype within the zebrafish brains. We also provide evidence that the BBB in zebrafish larva is molecularly and functionally intact and can interact with GBM cells in similar ways as in mammals  which together enables this model to accurately identify BBB penetrating drugs. Using GBM patients' samples  we further generate zebrafish patient derived orthotopic xenografts z PDOX and proof of concept experiments indicate the short term temozolomide response in z PDOX can predict the long term prognosis of corresponding GBM patients. These together illustrate the value of zebrafish GBM model in drug discovery and precision medicine. Overall design: 1.Single cell RNA seq for endothelial cells of zebrafish 2.Single cell RNA seq for GBM cells implanted in zebrafish brain", null, "pubmed:35199829", null, "Smartseq2 AXL A1 endo Danio", "GSM4432614", null, "tissue:endothelial cells|strain:flk:GFP|cell tye:endothelial cells", "Smartseq2 AXL A1 endo Danio", "ScRNA seq alignment process was completed by STAR 2.6.0a DESeq2 standard workflow Genome build: GRCz10 genome references for Zebrafish and GRCh38 genome references for human Supplementary files format and content: csv files with raw counts and FPKM", "endothelial cells", null, "1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope  the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope  a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle.   2. For GBM cells  zebrafish were injected with GBM U251 mCherry cells  and allowed to form widespread  tumor invasion for xxx 5 days. At that point  the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope  the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously  GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the 3\u2019 scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang  2010.", null, "strain:flk:GFP|cell tye:endothelial cells", "GSM4432614", "GSM4432614: Smartseq2 AXL A1 endo Danio; Danio rerio; RNA Seq", "GSM4432614", null, "1", "1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope  the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope  a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle.   2. For GBM cells  zebrafish were injected with GBM U251 mCherry cells  and allowed to form widespread  tumor invasion for xxx 5 days. At that point  the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope  the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously  GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the three prime scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang  2010.", "GEO Accession:GSM4432614", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP254020", null, null, "AXL-A1_HHVK7CCXY_L3_1.clean.fq.gz AXL-A1_HHVK7CCXY_L3_2.clean.fq.gz", "fastq fastq", 1017985800.0, 3393286.0, "GSM4432614 r1", "0:150 1:150", "A:297904574;C:190252853;G:199665607;T:330106549;N:56217", 150, 150, null, null, 297904574, 190252853, 199665607, 330106549, 56217, "SRX7998903", "SRS6376266", "SRA1059261", "GEO", "Chen & Liu Lab, State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University., Sichuan University", 2, 0.82827, 0.84942, 0.55392, 0.56701, 0.89029, 0.89394, 0.61422, 0.61422, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2020-03-25", "Larval", "Larval", "Endothelium", "Cardiovascular System"], [75610, "SRR24740771", "SRX20518083", "SRS17828039", "SRP439616", "PRJNA976345", "An organ specific angiogenic control mechanism for endothelial tailoring", "GSE233488", "Transcriptome Analysis", "To address the role of endothelial Wnt/\u00df catenin signaling in CNS angiogenesis  we compared the bulk transcriptomes of WT and Wnt/\u00df catenin signaling deficient PHBC endothelial cells  prior to CNS vascular invasion. To this end  we used three approaches to abrogate endothelial Wnt/\u00df catenin signaling: Morpholino mediated knock down of gpr124  reck or wnt7aa. We find that the expression of mmp25b is decreased in PHBC endothelial cells of all Wnt/\u00df catenin signaling deficient conditions as compared to the WT controls. Overall design: Tgfli1:Gal4ubs3;UAS:Kaederk8 embryos were injected at the single cell stage with Morpholinos targeting gpr124  reck  or wnt7aa. Prior to CNS vascular invasion 30 hpf  PHBC endothelial cells expressing the Kaede fluorescent protein  were photoconverted shifting green towards red fluorescence by exposere to a 405 nm laser nanobeam  specifically at the level of the PHBC. Subsequent embryo dissociation and FACS allowed for isolation of PHBC endothelial cells. RNA extraction and sequencing was performed on 4 samples per condition  each containing photoconverted PHBC endothelial cells of 80 embryos.", null, "pubmed:38570687", null, "PHBC endothelial cells 30 hpf  wnt7aa MO 4", "GSM7429341", null, "source name:Vascular endothelium|tissue:Vascular endothelium|cell line:PHBC endothelial cells|Stage:30 hpf|cell type:Endothelial cells|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8|genotype:wnt7aa MO|treatment:photoconverted|geo loc name:missing|collection date:missing", "PHBC endothelial cells 30 hpf  wnt7aa MO 4", "The resulting raw reads were assessed for quality  adapter content  and duplication rates with FastQC. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. 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\u2014outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package84. 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. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers activities at the Universal Protein Resource UniProt. Assembly: DanRer10 Supplementary files format and content: library size normlized counts", "Vascular endothelium", null, "RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250\u2013500\u2009pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.", null, "tissue:Vascular endothelium|cell line:PHBC endothelial cells|Stage:30 hpf|cell type:Endothelial cells|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8|genotype:wnt7aa MO|treatment:photoconverted", "GSM7429341", "GSM7429341: PHBC endothelial cells 30 hpf  wnt7aa MO 4; Danio rerio; RNA Seq", "GSM7429341 r1", "GSM7429341", "1", "RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250\u2013500\u2009pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP439616", null, "loader:fastq load.py", "F4_MO_wnt7aa_R1.fastq.gz F4_MO_wnt7aa_R2.fastq.gz", "fastq fastq", 3410657071.0, 22888059.0, "GSM7429341 r1", null, "A:930255790;C:774998735;G:770566602;T:932969311;N:1866633", null, null, null, null, 930255790, 774998735, 770566602, 932969311, 1866633, "SRX20518083", "SRS17828039", "SRA1644604", "MPI for heart and lung research", "MPI for heart and lung research", 2, 0.9278, 0.9295, 0.13464, 0.13259, 0.75345, 0.75694, 0.50275, 0.49844, 74, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2023-05-25", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [75611, "SRR24740772", "SRX20518082", "SRS17828038", "SRP439616", "PRJNA976345", "An organ specific angiogenic control mechanism for endothelial tailoring", "GSE233488", "Transcriptome Analysis", "To address the role of endothelial Wnt/\u00df catenin signaling in CNS angiogenesis  we compared the bulk transcriptomes of WT and Wnt/\u00df catenin signaling deficient PHBC endothelial cells  prior to CNS vascular invasion. To this end  we used three approaches to abrogate endothelial Wnt/\u00df catenin signaling: Morpholino mediated knock down of gpr124  reck or wnt7aa. We find that the expression of mmp25b is decreased in PHBC endothelial cells of all Wnt/\u00df catenin signaling deficient conditions as compared to the WT controls. Overall design: Tgfli1:Gal4ubs3;UAS:Kaederk8 embryos were injected at the single cell stage with Morpholinos targeting gpr124  reck  or wnt7aa. Prior to CNS vascular invasion 30 hpf  PHBC endothelial cells expressing the Kaede fluorescent protein  were photoconverted shifting green towards red fluorescence by exposere to a 405 nm laser nanobeam  specifically at the level of the PHBC. Subsequent embryo dissociation and FACS allowed for isolation of PHBC endothelial cells. RNA extraction and sequencing was performed on 4 samples per condition  each containing photoconverted PHBC endothelial cells of 80 embryos.", null, "pubmed:38570687", null, "PHBC endothelial cells 30 hpf  wnt7aa MO 3", "GSM7429340", null, "source name:Vascular endothelium|tissue:Vascular endothelium|cell line:PHBC endothelial cells|Stage:30 hpf|cell type:Endothelial cells|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8|genotype:wnt7aa MO|treatment:photoconverted|geo loc name:missing|collection date:missing", "PHBC endothelial cells 30 hpf  wnt7aa MO 3", "The resulting raw reads were assessed for quality  adapter content  and duplication rates with FastQC. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. 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\u2014outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package84. 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. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers activities at the Universal Protein Resource UniProt. Assembly: DanRer10 Supplementary files format and content: library size normlized counts", "Vascular endothelium", null, "RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250\u2013500\u2009pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.", null, "tissue:Vascular endothelium|cell line:PHBC endothelial cells|Stage:30 hpf|cell type:Endothelial cells|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8|genotype:wnt7aa MO|treatment:photoconverted", "GSM7429340", "GSM7429340: PHBC endothelial cells 30 hpf  wnt7aa MO 3; Danio rerio; RNA Seq", "GSM7429340 r1", "GSM7429340", "1", "RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250\u2013500\u2009pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP439616", null, "loader:fastq load.py", "F3_MO_wnt7aa_R1.fastq.gz F3_MO_wnt7aa_R2.fastq.gz", "fastq fastq", 2844102685.0, 19087245.0, "GSM7429340 r1", null, "A:753836724;C:664365246;G:664895731;T:759443497;N:1561487", null, null, null, null, 753836724, 664365246, 664895731, 759443497, 1561487, "SRX20518082", "SRS17828038", "SRA1644604", "MPI for heart and lung research", "MPI for heart and lung research", 2, 0.87882, 0.88191, 0.10969, 0.10713, 0.79397, 0.79557, 0.52306, 0.52523, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2023-05-25", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [75612, "SRR24740773", "SRX20518081", "SRS17828037", "SRP439616", "PRJNA976345", "An organ specific angiogenic control mechanism for endothelial tailoring", "GSE233488", "Transcriptome Analysis", "To address the role of endothelial Wnt/\u00df catenin signaling in CNS angiogenesis  we compared the bulk transcriptomes of WT and Wnt/\u00df catenin signaling deficient PHBC endothelial cells  prior to CNS vascular invasion. To this end  we used three approaches to abrogate endothelial Wnt/\u00df catenin signaling: Morpholino mediated knock down of gpr124  reck or wnt7aa. We find that the expression of mmp25b is decreased in PHBC endothelial cells of all Wnt/\u00df catenin signaling deficient conditions as compared to the WT controls. Overall design: Tgfli1:Gal4ubs3;UAS:Kaederk8 embryos were injected at the single cell stage with Morpholinos targeting gpr124  reck  or wnt7aa. Prior to CNS vascular invasion 30 hpf  PHBC endothelial cells expressing the Kaede fluorescent protein  were photoconverted shifting green towards red fluorescence by exposere to a 405 nm laser nanobeam  specifically at the level of the PHBC. Subsequent embryo dissociation and FACS allowed for isolation of PHBC endothelial cells. RNA extraction and sequencing was performed on 4 samples per condition  each containing photoconverted PHBC endothelial cells of 80 embryos.", null, "pubmed:38570687", null, "PHBC endothelial cells 30 hpf  wnt7aa MO 2", "GSM7429339", null, "source name:Vascular endothelium|tissue:Vascular endothelium|cell line:PHBC endothelial cells|Stage:30 hpf|cell type:Endothelial cells|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8|genotype:wnt7aa MO|treatment:photoconverted|geo loc name:missing|collection date:missing", "PHBC endothelial cells 30 hpf  wnt7aa MO 2", "The resulting raw reads were assessed for quality  adapter content  and duplication rates with FastQC. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. 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\u2014outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package84. 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. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers activities at the Universal Protein Resource UniProt. Assembly: DanRer10 Supplementary files format and content: library size normlized counts", "Vascular endothelium", null, "RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250\u2013500\u2009pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.", null, "tissue:Vascular endothelium|cell line:PHBC endothelial cells|Stage:30 hpf|cell type:Endothelial cells|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8|genotype:wnt7aa MO|treatment:photoconverted", "GSM7429339", "GSM7429339: PHBC endothelial cells 30 hpf  wnt7aa MO 2; Danio rerio; RNA Seq", "GSM7429339 r1", "GSM7429339", "1", "RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250\u2013500\u2009pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP439616", null, "loader:fastq load.py", "F2_MO_wnt7aa_R1.fastq.gz F2_MO_wnt7aa_R2.fastq.gz", "fastq fastq", 3003877741.0, 20155237.0, "GSM7429339 r1", null, "A:806731621;C:691626094;G:690105872;T:813757253;N:1656901", null, null, null, null, 806731621, 691626094, 690105872, 813757253, 1656901, "SRX20518081", "SRS17828037", "SRA1644604", "MPI for heart and lung research", "MPI for heart and lung research", 2, 0.88411, 0.88628, 0.15488, 0.15267, 0.77654, 0.77891, 0.5348, 0.5414, 73, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2023-05-25", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [75613, "SRR24740774", "SRX20518080", "SRS17828036", "SRP439616", "PRJNA976345", "An organ specific angiogenic control mechanism for endothelial tailoring", "GSE233488", "Transcriptome Analysis", "To address the role of endothelial Wnt/\u00df catenin signaling in CNS angiogenesis  we compared the bulk transcriptomes of WT and Wnt/\u00df catenin signaling deficient PHBC endothelial cells  prior to CNS vascular invasion. To this end  we used three approaches to abrogate endothelial Wnt/\u00df catenin signaling: Morpholino mediated knock down of gpr124  reck or wnt7aa. We find that the expression of mmp25b is decreased in PHBC endothelial cells of all Wnt/\u00df catenin signaling deficient conditions as compared to the WT controls. Overall design: Tgfli1:Gal4ubs3;UAS:Kaederk8 embryos were injected at the single cell stage with Morpholinos targeting gpr124  reck  or wnt7aa. Prior to CNS vascular invasion 30 hpf  PHBC endothelial cells expressing the Kaede fluorescent protein  were photoconverted shifting green towards red fluorescence by exposere to a 405 nm laser nanobeam  specifically at the level of the PHBC. Subsequent embryo dissociation and FACS allowed for isolation of PHBC endothelial cells. RNA extraction and sequencing was performed on 4 samples per condition  each containing photoconverted PHBC endothelial cells of 80 embryos.", null, "pubmed:38570687", null, "PHBC endothelial cells 30 hpf  wnt7aa MO 1", "GSM7429338", null, "source name:Vascular endothelium|tissue:Vascular endothelium|cell line:PHBC endothelial cells|Stage:30 hpf|cell type:Endothelial cells|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8|genotype:wnt7aa MO|treatment:photoconverted|geo loc name:missing|collection date:missing", "PHBC endothelial cells 30 hpf  wnt7aa MO 1", "The resulting raw reads were assessed for quality  adapter content  and duplication rates with FastQC. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. 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\u2014outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package84. 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. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers activities at the Universal Protein Resource UniProt. Assembly: DanRer10 Supplementary files format and content: library size normlized counts", "Vascular endothelium", null, "RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250\u2013500\u2009pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.", null, "tissue:Vascular endothelium|cell line:PHBC endothelial cells|Stage:30 hpf|cell type:Endothelial cells|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8|genotype:wnt7aa MO|treatment:photoconverted", "GSM7429338", "GSM7429338: PHBC endothelial cells 30 hpf  wnt7aa MO 1; Danio rerio; RNA Seq", "GSM7429338 r1", "GSM7429338", "1", "RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250\u2013500\u2009pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP439616", null, "loader:fastq load.py", "F1_MO_wnt7aa_R1.fastq.gz F1_MO_wnt7aa_R2.fastq.gz", "fastq fastq", 2134056620.0, 14319615.0, "GSM7429338 r1", null, "A:574764769;C:489478372;G:488808981;T:579820041;N:1184457", null, null, null, null, 574764769, 489478372, 488808981, 579820041, 1184457, "SRX20518080", "SRS17828036", "SRA1644604", "MPI for heart and lung research", "MPI for heart and lung research", 2, 0.90992, 0.91125, 0.15485, 0.15169, 0.77126, 0.77352, 0.52889, 0.52569, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2023-05-25", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [75614, "SRR24740775", "SRX20518079", "SRS17828035", "SRP439616", "PRJNA976345", "An organ specific angiogenic control mechanism for endothelial tailoring", "GSE233488", "Transcriptome Analysis", "To address the role of endothelial Wnt/\u00df catenin signaling in CNS angiogenesis  we compared the bulk transcriptomes of WT and Wnt/\u00df catenin signaling deficient PHBC endothelial cells  prior to CNS vascular invasion. To this end  we used three approaches to abrogate endothelial Wnt/\u00df catenin signaling: Morpholino mediated knock down of gpr124  reck or wnt7aa. We find that the expression of mmp25b is decreased in PHBC endothelial cells of all Wnt/\u00df catenin signaling deficient conditions as compared to the WT controls. Overall design: Tgfli1:Gal4ubs3;UAS:Kaederk8 embryos were injected at the single cell stage with Morpholinos targeting gpr124  reck  or wnt7aa. Prior to CNS vascular invasion 30 hpf  PHBC endothelial cells expressing the Kaede fluorescent protein  were photoconverted shifting green towards red fluorescence by exposere to a 405 nm laser nanobeam  specifically at the level of the PHBC. Subsequent embryo dissociation and FACS allowed for isolation of PHBC endothelial cells. RNA extraction and sequencing was performed on 4 samples per condition  each containing photoconverted PHBC endothelial cells of 80 embryos.", null, "pubmed:38570687", null, "PHBC endothelial cells 30 hpf  reck MO 4", "GSM7429337", null, "source name:Vascular endothelium|tissue:Vascular endothelium|cell line:PHBC endothelial cells|Stage:30 hpf|cell type:Endothelial cells|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8|genotype:reck MO|treatment:photoconverted|geo loc name:missing|collection date:missing", "PHBC endothelial cells 30 hpf  reck MO 4", "The resulting raw reads were assessed for quality  adapter content  and duplication rates with FastQC. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. 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\u2014outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package84. 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. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers activities at the Universal Protein Resource UniProt. Assembly: DanRer10 Supplementary files format and content: library size normlized counts", "Vascular endothelium", null, "RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250\u2013500\u2009pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.", null, "tissue:Vascular endothelium|cell line:PHBC endothelial cells|Stage:30 hpf|cell type:Endothelial cells|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8|genotype:reck MO|treatment:photoconverted", "GSM7429337", "GSM7429337: PHBC endothelial cells 30 hpf  reck MO 4; Danio rerio; RNA Seq", "GSM7429337 r1", "GSM7429337", "1", "RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250\u2013500\u2009pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP439616", null, "loader:fastq load.py", "E4_MO_reck_R1.fastq.gz E4_MO_reck_R2.fastq.gz", "fastq fastq", 2600213337.0, 17457111.0, "GSM7429337 r1", null, "A:711797268;C:588127202;G:584757641;T:714124587;N:1406639", null, null, null, null, 711797268, 588127202, 584757641, 714124587, 1406639, "SRX20518079", "SRS17828035", "SRA1644604", "MPI for heart and lung research", "MPI for heart and lung research", 2, 0.90425, 0.905, 0.13217, 0.13087, 0.74245, 0.74692, 0.47354, 0.48629, 74, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2023-05-25", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [75615, "SRR24740776", "SRX20518078", "SRS17828034", "SRP439616", "PRJNA976345", "An organ specific angiogenic control mechanism for endothelial tailoring", "GSE233488", "Transcriptome Analysis", "To address the role of endothelial Wnt/\u00df catenin signaling in CNS angiogenesis  we compared the bulk transcriptomes of WT and Wnt/\u00df catenin signaling deficient PHBC endothelial cells  prior to CNS vascular invasion. To this end  we used three approaches to abrogate endothelial Wnt/\u00df catenin signaling: Morpholino mediated knock down of gpr124  reck or wnt7aa. We find that the expression of mmp25b is decreased in PHBC endothelial cells of all Wnt/\u00df catenin signaling deficient conditions as compared to the WT controls. Overall design: Tgfli1:Gal4ubs3;UAS:Kaederk8 embryos were injected at the single cell stage with Morpholinos targeting gpr124  reck  or wnt7aa. Prior to CNS vascular invasion 30 hpf  PHBC endothelial cells expressing the Kaede fluorescent protein  were photoconverted shifting green towards red fluorescence by exposere to a 405 nm laser nanobeam  specifically at the level of the PHBC. Subsequent embryo dissociation and FACS allowed for isolation of PHBC endothelial cells. RNA extraction and sequencing was performed on 4 samples per condition  each containing photoconverted PHBC endothelial cells of 80 embryos.", null, "pubmed:38570687", null, "PHBC endothelial cells 30 hpf  reck MO 3", "GSM7429336", null, "source name:Vascular endothelium|tissue:Vascular endothelium|cell line:PHBC endothelial cells|Stage:30 hpf|cell type:Endothelial cells|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8|genotype:reck MO|treatment:photoconverted|geo loc name:missing|collection date:missing", "PHBC endothelial cells 30 hpf  reck MO 3", "The resulting raw reads were assessed for quality  adapter content  and duplication rates with FastQC. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. 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\u2014outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package84. 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. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers activities at the Universal Protein Resource UniProt. Assembly: DanRer10 Supplementary files format and content: library size normlized counts", "Vascular endothelium", null, "RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250\u2013500\u2009pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.", null, "tissue:Vascular endothelium|cell line:PHBC endothelial cells|Stage:30 hpf|cell type:Endothelial cells|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8|genotype:reck MO|treatment:photoconverted", "GSM7429336", "GSM7429336: PHBC endothelial cells 30 hpf  reck MO 3; Danio rerio; RNA Seq", "GSM7429336 r1", "GSM7429336", "1", "RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250\u2013500\u2009pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP439616", null, "loader:fastq load.py", "E3_MO_reck_R1.fastq.gz E3_MO_reck_R2.fastq.gz", "fastq fastq", 1741572044.0, 11687076.0, "GSM7429336 r1", null, "A:472997022;C:397732899;G:395569364;T:474320408;N:952351", null, null, null, null, 472997022, 397732899, 395569364, 474320408, 952351, "SRX20518078", "SRS17828034", "SRA1644604", "MPI for heart and lung research", "MPI for heart and lung research", 2, 0.93581, 0.93755, 0.1129, 0.11226, 0.7559, 0.75801, 0.48017, 0.47999, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2023-05-25", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [75616, "SRR24740777", "SRX20518077", "SRS17828033", "SRP439616", "PRJNA976345", "An organ specific angiogenic control mechanism for endothelial tailoring", "GSE233488", "Transcriptome Analysis", "To address the role of endothelial Wnt/\u00df catenin signaling in CNS angiogenesis  we compared the bulk transcriptomes of WT and Wnt/\u00df catenin signaling deficient PHBC endothelial cells  prior to CNS vascular invasion. To this end  we used three approaches to abrogate endothelial Wnt/\u00df catenin signaling: Morpholino mediated knock down of gpr124  reck or wnt7aa. We find that the expression of mmp25b is decreased in PHBC endothelial cells of all Wnt/\u00df catenin signaling deficient conditions as compared to the WT controls. Overall design: Tgfli1:Gal4ubs3;UAS:Kaederk8 embryos were injected at the single cell stage with Morpholinos targeting gpr124  reck  or wnt7aa. Prior to CNS vascular invasion 30 hpf  PHBC endothelial cells expressing the Kaede fluorescent protein  were photoconverted shifting green towards red fluorescence by exposere to a 405 nm laser nanobeam  specifically at the level of the PHBC. Subsequent embryo dissociation and FACS allowed for isolation of PHBC endothelial cells. RNA extraction and sequencing was performed on 4 samples per condition  each containing photoconverted PHBC endothelial cells of 80 embryos.", null, "pubmed:38570687", null, "PHBC endothelial cells 30 hpf  reck MO 2", "GSM7429335", null, "source name:Vascular endothelium|tissue:Vascular endothelium|cell line:PHBC endothelial cells|Stage:30 hpf|cell type:Endothelial cells|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8|genotype:reck MO|treatment:photoconverted|geo loc name:missing|collection date:missing", "PHBC endothelial cells 30 hpf  reck MO 2", "The resulting raw reads were assessed for quality  adapter content  and duplication rates with FastQC. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. 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\u2014outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package84. 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. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers activities at the Universal Protein Resource UniProt. Assembly: DanRer10 Supplementary files format and content: library size normlized counts", "Vascular endothelium", null, "RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250\u2013500\u2009pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.", null, "tissue:Vascular endothelium|cell line:PHBC endothelial cells|Stage:30 hpf|cell type:Endothelial cells|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8|genotype:reck MO|treatment:photoconverted", "GSM7429335", "GSM7429335: PHBC endothelial cells 30 hpf  reck MO 2; Danio rerio; RNA Seq", "GSM7429335 r1", "GSM7429335", "1", "RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250\u2013500\u2009pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP439616", null, "loader:fastq load.py", "E2_MO_reck_R1.fastq.gz E2_MO_reck_R2.fastq.gz", "fastq fastq", 2671658198.0, 17928556.0, "GSM7429335 r1", null, "A:725812218;C:610551715;G:606842688;T:726993096;N:1458481", null, null, null, null, 725812218, 610551715, 606842688, 726993096, 1458481, "SRX20518077", "SRS17828033", "SRA1644604", "MPI for heart and lung research", "MPI for heart and lung research", 2, 0.92509, 0.92531, 0.13119, 0.13003, 0.74487, 0.74854, 0.47968, 0.48136, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2023-05-25", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [75617, "SRR24740778", "SRX20518076", "SRS17828032", "SRP439616", "PRJNA976345", "An organ specific angiogenic control mechanism for endothelial tailoring", "GSE233488", "Transcriptome Analysis", "To address the role of endothelial Wnt/\u00df catenin signaling in CNS angiogenesis  we compared the bulk transcriptomes of WT and Wnt/\u00df catenin signaling deficient PHBC endothelial cells  prior to CNS vascular invasion. To this end  we used three approaches to abrogate endothelial Wnt/\u00df catenin signaling: Morpholino mediated knock down of gpr124  reck or wnt7aa. We find that the expression of mmp25b is decreased in PHBC endothelial cells of all Wnt/\u00df catenin signaling deficient conditions as compared to the WT controls. Overall design: Tgfli1:Gal4ubs3;UAS:Kaederk8 embryos were injected at the single cell stage with Morpholinos targeting gpr124  reck  or wnt7aa. Prior to CNS vascular invasion 30 hpf  PHBC endothelial cells expressing the Kaede fluorescent protein  were photoconverted shifting green towards red fluorescence by exposere to a 405 nm laser nanobeam  specifically at the level of the PHBC. Subsequent embryo dissociation and FACS allowed for isolation of PHBC endothelial cells. RNA extraction and sequencing was performed on 4 samples per condition  each containing photoconverted PHBC endothelial cells of 80 embryos.", null, "pubmed:38570687", null, "PHBC endothelial cells 30 hpf  reck MO 1", "GSM7429334", null, "source name:Vascular endothelium|tissue:Vascular endothelium|cell line:PHBC endothelial cells|Stage:30 hpf|cell type:Endothelial cells|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8|genotype:reck MO|treatment:photoconverted|geo loc name:missing|collection date:missing", "PHBC endothelial cells 30 hpf  reck MO 1", "The resulting raw reads were assessed for quality  adapter content  and duplication rates with FastQC. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. 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\u2014outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package84. 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. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers activities at the Universal Protein Resource UniProt. Assembly: DanRer10 Supplementary files format and content: library size normlized counts", "Vascular endothelium", null, "RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250\u2013500\u2009pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.", null, "tissue:Vascular endothelium|cell line:PHBC endothelial cells|Stage:30 hpf|cell type:Endothelial cells|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8|genotype:reck MO|treatment:photoconverted", "GSM7429334", "GSM7429334: PHBC endothelial cells 30 hpf  reck MO 1; Danio rerio; RNA Seq", "GSM7429334 r1", "GSM7429334", "1", "RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250\u2013500\u2009pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP439616", null, "loader:fastq load.py", "E1_MO_reck_R1.fastq.gz E1_MO_reck_R2.fastq.gz", "fastq fastq", 2779576944.0, 19473447.0, "GSM7429334 r1", null, "A:818491725;C:569735041;G:564250518;T:825468450;N:1631210", null, null, null, null, 818491725, 569735041, 564250518, 825468450, 1631210, "SRX20518076", "SRS17828032", "SRA1644604", "MPI for heart and lung research", "MPI for heart and lung research", 2, 0.60589, 0.60513, 0.08903, 0.0878, 0.80093, 0.80391, 0.50318, 0.48591, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2023-05-25", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [75618, "SRR24740779", "SRX20518075", "SRS17828031", "SRP439616", "PRJNA976345", "An organ specific angiogenic control mechanism for endothelial tailoring", "GSE233488", "Transcriptome Analysis", "To address the role of endothelial Wnt/\u00df catenin signaling in CNS angiogenesis  we compared the bulk transcriptomes of WT and Wnt/\u00df catenin signaling deficient PHBC endothelial cells  prior to CNS vascular invasion. To this end  we used three approaches to abrogate endothelial Wnt/\u00df catenin signaling: Morpholino mediated knock down of gpr124  reck or wnt7aa. We find that the expression of mmp25b is decreased in PHBC endothelial cells of all Wnt/\u00df catenin signaling deficient conditions as compared to the WT controls. Overall design: Tgfli1:Gal4ubs3;UAS:Kaederk8 embryos were injected at the single cell stage with Morpholinos targeting gpr124  reck  or wnt7aa. Prior to CNS vascular invasion 30 hpf  PHBC endothelial cells expressing the Kaede fluorescent protein  were photoconverted shifting green towards red fluorescence by exposere to a 405 nm laser nanobeam  specifically at the level of the PHBC. Subsequent embryo dissociation and FACS allowed for isolation of PHBC endothelial cells. RNA extraction and sequencing was performed on 4 samples per condition  each containing photoconverted PHBC endothelial cells of 80 embryos.", null, "pubmed:38570687", null, "PHBC endothelial cells 30 hpf  TF MO 4", "GSM7429333", null, "source name:Vascular endothelium|tissue:Vascular endothelium|cell line:PHBC endothelial cells|Stage:30 hpf|cell type:Endothelial cells|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8|genotype:TF MO|treatment:photoconverted|geo loc name:missing|collection date:missing", "PHBC endothelial cells 30 hpf  TF MO 4", "The resulting raw reads were assessed for quality  adapter content  and duplication rates with FastQC. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. 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\u2014outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package84. 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. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers activities at the Universal Protein Resource UniProt. Assembly: DanRer10 Supplementary files format and content: library size normlized counts", "Vascular endothelium", null, "RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250\u2013500\u2009pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.", null, "tissue:Vascular endothelium|cell line:PHBC endothelial cells|Stage:30 hpf|cell type:Endothelial cells|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8|genotype:TF MO|treatment:photoconverted", "GSM7429333", "GSM7429333: PHBC endothelial cells 30 hpf  TF MO 4; Danio rerio; RNA Seq", "GSM7429333 r1", "GSM7429333", "1", "RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250\u2013500\u2009pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP439616", null, "loader:fastq load.py", "D4_MO_TF_R1.fastq.gz D4_MO_TF_R2.fastq.gz", "fastq fastq", 3262028321.0, 21890211.0, "GSM7429333 r1", null, "A:876880120;C:749366908;G:748032046;T:885943266;N:1805981", null, null, null, null, 876880120, 749366908, 748032046, 885943266, 1805981, "SRX20518075", "SRS17828031", "SRA1644604", "MPI for heart and lung research", "MPI for heart and lung research", 2, 0.90243, 0.90467, 0.15799, 0.15728, 0.77218, 0.77524, 0.54673, 0.54717, 75, 74, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2023-05-25", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [75619, "SRR24740780", "SRX20518074", "SRS17828030", "SRP439616", "PRJNA976345", "An organ specific angiogenic control mechanism for endothelial tailoring", "GSE233488", "Transcriptome Analysis", "To address the role of endothelial Wnt/\u00df catenin signaling in CNS angiogenesis  we compared the bulk transcriptomes of WT and Wnt/\u00df catenin signaling deficient PHBC endothelial cells  prior to CNS vascular invasion. To this end  we used three approaches to abrogate endothelial Wnt/\u00df catenin signaling: Morpholino mediated knock down of gpr124  reck or wnt7aa. We find that the expression of mmp25b is decreased in PHBC endothelial cells of all Wnt/\u00df catenin signaling deficient conditions as compared to the WT controls. Overall design: Tgfli1:Gal4ubs3;UAS:Kaederk8 embryos were injected at the single cell stage with Morpholinos targeting gpr124  reck  or wnt7aa. Prior to CNS vascular invasion 30 hpf  PHBC endothelial cells expressing the Kaede fluorescent protein  were photoconverted shifting green towards red fluorescence by exposere to a 405 nm laser nanobeam  specifically at the level of the PHBC. Subsequent embryo dissociation and FACS allowed for isolation of PHBC endothelial cells. RNA extraction and sequencing was performed on 4 samples per condition  each containing photoconverted PHBC endothelial cells of 80 embryos.", null, "pubmed:38570687", null, "PHBC endothelial cells 30 hpf  TF MO 3", "GSM7429332", null, "source name:Vascular endothelium|tissue:Vascular endothelium|cell line:PHBC endothelial cells|Stage:30 hpf|cell type:Endothelial cells|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8|genotype:TF MO|treatment:photoconverted|geo loc name:missing|collection date:missing", "PHBC endothelial cells 30 hpf  TF MO 3", "The resulting raw reads were assessed for quality  adapter content  and duplication rates with FastQC. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. 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\u2014outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package84. 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. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers activities at the Universal Protein Resource UniProt. Assembly: DanRer10 Supplementary files format and content: library size normlized counts", "Vascular endothelium", null, "RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250\u2013500\u2009pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.", null, "tissue:Vascular endothelium|cell line:PHBC endothelial cells|Stage:30 hpf|cell type:Endothelial cells|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8|genotype:TF MO|treatment:photoconverted", "GSM7429332", "GSM7429332: PHBC endothelial cells 30 hpf  TF MO 3; Danio rerio; RNA Seq", "GSM7429332 r1", "GSM7429332", "1", "RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250\u2013500\u2009pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP439616", null, "loader:fastq load.py", "D3_MO_TF_R1.fastq.gz D3_MO_TF_R2.fastq.gz", "fastq fastq", 911957449.0, 6119680.0, "GSM7429332 r1", null, "A:240966620;C:213588458;G:213137469;T:243759752;N:505150", null, null, null, null, 240966620, 213588458, 213137469, 243759752, 505150, "SRX20518074", "SRS17828030", "SRA1644604", "MPI for heart and lung research", "MPI for heart and lung research", 2, 0.88163, 0.88298, 0.13578, 0.13347, 0.77977, 0.7837, 0.53317, 0.5412, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2023-05-25", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [75620, "SRR24740781", "SRX20518073", "SRS17828029", "SRP439616", "PRJNA976345", "An organ specific angiogenic control mechanism for endothelial tailoring", "GSE233488", "Transcriptome Analysis", "To address the role of endothelial Wnt/\u00df catenin signaling in CNS angiogenesis  we compared the bulk transcriptomes of WT and Wnt/\u00df catenin signaling deficient PHBC endothelial cells  prior to CNS vascular invasion. To this end  we used three approaches to abrogate endothelial Wnt/\u00df catenin signaling: Morpholino mediated knock down of gpr124  reck or wnt7aa. We find that the expression of mmp25b is decreased in PHBC endothelial cells of all Wnt/\u00df catenin signaling deficient conditions as compared to the WT controls. Overall design: Tgfli1:Gal4ubs3;UAS:Kaederk8 embryos were injected at the single cell stage with Morpholinos targeting gpr124  reck  or wnt7aa. Prior to CNS vascular invasion 30 hpf  PHBC endothelial cells expressing the Kaede fluorescent protein  were photoconverted shifting green towards red fluorescence by exposere to a 405 nm laser nanobeam  specifically at the level of the PHBC. Subsequent embryo dissociation and FACS allowed for isolation of PHBC endothelial cells. RNA extraction and sequencing was performed on 4 samples per condition  each containing photoconverted PHBC endothelial cells of 80 embryos.", null, "pubmed:38570687", null, "PHBC endothelial cells 30 hpf  TF MO 2", "GSM7429331", null, "source name:Vascular endothelium|tissue:Vascular endothelium|cell line:PHBC endothelial cells|Stage:30 hpf|cell type:Endothelial cells|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8|genotype:TF MO|treatment:photoconverted|geo loc name:missing|collection date:missing", "PHBC endothelial cells 30 hpf  TF MO 2", "The resulting raw reads were assessed for quality  adapter content  and duplication rates with FastQC. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. 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\u2014outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package84. 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. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers activities at the Universal Protein Resource UniProt. Assembly: DanRer10 Supplementary files format and content: library size normlized counts", "Vascular endothelium", null, "RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250\u2013500\u2009pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.", null, "tissue:Vascular endothelium|cell line:PHBC endothelial cells|Stage:30 hpf|cell type:Endothelial cells|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8|genotype:TF MO|treatment:photoconverted", "GSM7429331", "GSM7429331: PHBC endothelial cells 30 hpf  TF MO 2; Danio rerio; RNA Seq", "GSM7429331 r1", "GSM7429331", "1", "RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250\u2013500\u2009pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP439616", null, "loader:fastq load.py", "D2_MO_TF_R1.fastq.gz D2_MO_TF_R2.fastq.gz", "fastq fastq", 2828207009.0, 18989270.0, "GSM7429331 r1", null, "A:742830477;C:672427123;G:669193099;T:742200169;N:1556141", null, null, null, null, 742830477, 672427123, 669193099, 742200169, 1556141, "SRX20518073", "SRS17828029", "SRA1644604", "MPI for heart and lung research", "MPI for heart and lung research", 2, 0.8578, 0.86018, 0.08003, 0.07945, 0.8016, 0.80359, 0.47591, 0.47619, 74, 73, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2023-05-25", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [75621, "SRR24740782", "SRX20518072", "SRS17828028", "SRP439616", "PRJNA976345", "An organ specific angiogenic control mechanism for endothelial tailoring", "GSE233488", "Transcriptome Analysis", "To address the role of endothelial Wnt/\u00df catenin signaling in CNS angiogenesis  we compared the bulk transcriptomes of WT and Wnt/\u00df catenin signaling deficient PHBC endothelial cells  prior to CNS vascular invasion. To this end  we used three approaches to abrogate endothelial Wnt/\u00df catenin signaling: Morpholino mediated knock down of gpr124  reck or wnt7aa. We find that the expression of mmp25b is decreased in PHBC endothelial cells of all Wnt/\u00df catenin signaling deficient conditions as compared to the WT controls. Overall design: Tgfli1:Gal4ubs3;UAS:Kaederk8 embryos were injected at the single cell stage with Morpholinos targeting gpr124  reck  or wnt7aa. Prior to CNS vascular invasion 30 hpf  PHBC endothelial cells expressing the Kaede fluorescent protein  were photoconverted shifting green towards red fluorescence by exposere to a 405 nm laser nanobeam  specifically at the level of the PHBC. Subsequent embryo dissociation and FACS allowed for isolation of PHBC endothelial cells. RNA extraction and sequencing was performed on 4 samples per condition  each containing photoconverted PHBC endothelial cells of 80 embryos.", null, "pubmed:38570687", null, "PHBC endothelial cells 30 hpf  TF MO 1", "GSM7429330", null, "source name:Vascular endothelium|tissue:Vascular endothelium|cell line:PHBC endothelial cells|Stage:30 hpf|cell type:Endothelial cells|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8|genotype:TF MO|treatment:photoconverted|geo loc name:missing|collection date:missing", "PHBC endothelial cells 30 hpf  TF MO 1", "The resulting raw reads were assessed for quality  adapter content  and duplication rates with FastQC. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. 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\u2014outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package84. 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. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers activities at the Universal Protein Resource UniProt. Assembly: DanRer10 Supplementary files format and content: library size normlized counts", "Vascular endothelium", null, "RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250\u2013500\u2009pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.", null, "tissue:Vascular endothelium|cell line:PHBC endothelial cells|Stage:30 hpf|cell type:Endothelial cells|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8|genotype:TF MO|treatment:photoconverted", "GSM7429330", "GSM7429330: PHBC endothelial cells 30 hpf  TF MO 1; Danio rerio; RNA Seq", "GSM7429330 r1", "GSM7429330", "1", "RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250\u2013500\u2009pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP439616", null, "loader:fastq load.py", "D1_MO_TF_R1.fastq.gz D1_MO_TF_R2.fastq.gz", "fastq fastq", 3219964468.0, 21606481.0, "GSM7429330 r1", null, "A:865281524;C:741783926;G:739687813;T:871436747;N:1774458", null, null, null, null, 865281524, 741783926, 739687813, 871436747, 1774458, "SRX20518072", "SRS17828028", "SRA1644604", "MPI for heart and lung research", "MPI for heart and lung research", 2, 0.90355, 0.9049, 0.12506, 0.12473, 0.76469, 0.76891, 0.5213, 0.51875, 72, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2023-05-25", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [75622, "SRR24740783", "SRX20518071", "SRS17828027", "SRP439616", "PRJNA976345", "An organ specific angiogenic control mechanism for endothelial tailoring", "GSE233488", "Transcriptome Analysis", "To address the role of endothelial Wnt/\u00df catenin signaling in CNS angiogenesis  we compared the bulk transcriptomes of WT and Wnt/\u00df catenin signaling deficient PHBC endothelial cells  prior to CNS vascular invasion. To this end  we used three approaches to abrogate endothelial Wnt/\u00df catenin signaling: Morpholino mediated knock down of gpr124  reck or wnt7aa. We find that the expression of mmp25b is decreased in PHBC endothelial cells of all Wnt/\u00df catenin signaling deficient conditions as compared to the WT controls. Overall design: Tgfli1:Gal4ubs3;UAS:Kaederk8 embryos were injected at the single cell stage with Morpholinos targeting gpr124  reck  or wnt7aa. Prior to CNS vascular invasion 30 hpf  PHBC endothelial cells expressing the Kaede fluorescent protein  were photoconverted shifting green towards red fluorescence by exposere to a 405 nm laser nanobeam  specifically at the level of the PHBC. Subsequent embryo dissociation and FACS allowed for isolation of PHBC endothelial cells. RNA extraction and sequencing was performed on 4 samples per condition  each containing photoconverted PHBC endothelial cells of 80 embryos.", null, "pubmed:38570687", null, "PHBC endothelial cells 30 hpf  gpr124 MO 4", "GSM7429329", null, "source name:Vascular endothelium|tissue:Vascular endothelium|cell line:PHBC endothelial cells|Stage:30 hpf|cell type:Endothelial cells|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8|genotype:gpr124 MO|treatment:photoconverted|geo loc name:missing|collection date:missing", "PHBC endothelial cells 30 hpf  gpr124 MO 4", "The resulting raw reads were assessed for quality  adapter content  and duplication rates with FastQC. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. 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\u2014outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package84. 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. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers activities at the Universal Protein Resource UniProt. Assembly: DanRer10 Supplementary files format and content: library size normlized counts", "Vascular endothelium", null, "RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250\u2013500\u2009pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.", null, "tissue:Vascular endothelium|cell line:PHBC endothelial cells|Stage:30 hpf|cell type:Endothelial cells|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8|genotype:gpr124 MO|treatment:photoconverted", "GSM7429329", "GSM7429329: PHBC endothelial cells 30 hpf  gpr124 MO 4; Danio rerio; RNA Seq", "GSM7429329 r1", "GSM7429329", "1", "RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250\u2013500\u2009pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP439616", null, "loader:fastq load.py", "C4_MO_gpr124_R1.fastq.gz C4_MO_gpr124_R2.fastq.gz", "fastq fastq", 2735180426.0, 18351837.0, "GSM7429329 r1", null, "A:727609254;C:631295729;G:635633455;T:739158077;N:1483911", null, null, null, null, 727609254, 631295729, 635633455, 739158077, 1483911, "SRX20518071", "SRS17828027", "SRA1644604", "MPI for heart and lung research", "MPI for heart and lung research", 2, 0.87574, 0.88067, 0.18017, 0.17428, 0.81091, 0.81345, 0.51599, 0.50175, 72, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2023-05-25", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [75623, "SRR24740784", "SRX20518070", "SRS17828026", "SRP439616", "PRJNA976345", "An organ specific angiogenic control mechanism for endothelial tailoring", "GSE233488", "Transcriptome Analysis", "To address the role of endothelial Wnt/\u00df catenin signaling in CNS angiogenesis  we compared the bulk transcriptomes of WT and Wnt/\u00df catenin signaling deficient PHBC endothelial cells  prior to CNS vascular invasion. To this end  we used three approaches to abrogate endothelial Wnt/\u00df catenin signaling: Morpholino mediated knock down of gpr124  reck or wnt7aa. We find that the expression of mmp25b is decreased in PHBC endothelial cells of all Wnt/\u00df catenin signaling deficient conditions as compared to the WT controls. Overall design: Tgfli1:Gal4ubs3;UAS:Kaederk8 embryos were injected at the single cell stage with Morpholinos targeting gpr124  reck  or wnt7aa. Prior to CNS vascular invasion 30 hpf  PHBC endothelial cells expressing the Kaede fluorescent protein  were photoconverted shifting green towards red fluorescence by exposere to a 405 nm laser nanobeam  specifically at the level of the PHBC. Subsequent embryo dissociation and FACS allowed for isolation of PHBC endothelial cells. RNA extraction and sequencing was performed on 4 samples per condition  each containing photoconverted PHBC endothelial cells of 80 embryos.", null, "pubmed:38570687", null, "PHBC endothelial cells 30 hpf  gpr124 MO 3", "GSM7429328", null, "source name:Vascular endothelium|tissue:Vascular endothelium|cell line:PHBC endothelial cells|Stage:30 hpf|cell type:Endothelial cells|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8|genotype:gpr124 MO|treatment:photoconverted|geo loc name:missing|collection date:missing", "PHBC endothelial cells 30 hpf  gpr124 MO 3", "The resulting raw reads were assessed for quality  adapter content  and duplication rates with FastQC. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. 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\u2014outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package84. 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. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers activities at the Universal Protein Resource UniProt. Assembly: DanRer10 Supplementary files format and content: library size normlized counts", "Vascular endothelium", null, "RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250\u2013500\u2009pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.", null, "tissue:Vascular endothelium|cell line:PHBC endothelial cells|Stage:30 hpf|cell type:Endothelial cells|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8|genotype:gpr124 MO|treatment:photoconverted", "GSM7429328", "GSM7429328: PHBC endothelial cells 30 hpf  gpr124 MO 3; Danio rerio; RNA Seq", "GSM7429328 r1", "GSM7429328", "1", "RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250\u2013500\u2009pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP439616", null, "loader:fastq load.py", "C3_MO_gpr124_R1.fastq.gz C3_MO_gpr124_R2.fastq.gz", "fastq fastq", 2832145279.0, 19001125.0, "GSM7429328 r1", null, "A:742506972;C:669366817;G:669405672;T:749307010;N:1558808", null, null, null, null, 742506972, 669366817, 669405672, 749307010, 1558808, "SRX20518070", "SRS17828026", "SRA1644604", "MPI for heart and lung research", "MPI for heart and lung research", 2, 0.86374, 0.86649, 0.12603, 0.12479, 0.78699, 0.78971, 0.53138, 0.53587, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2023-05-25", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [75624, "SRR24740785", "SRX20518069", "SRS17828025", "SRP439616", "PRJNA976345", "An organ specific angiogenic control mechanism for endothelial tailoring", "GSE233488", "Transcriptome Analysis", "To address the role of endothelial Wnt/\u00df catenin signaling in CNS angiogenesis  we compared the bulk transcriptomes of WT and Wnt/\u00df catenin signaling deficient PHBC endothelial cells  prior to CNS vascular invasion. To this end  we used three approaches to abrogate endothelial Wnt/\u00df catenin signaling: Morpholino mediated knock down of gpr124  reck or wnt7aa. We find that the expression of mmp25b is decreased in PHBC endothelial cells of all Wnt/\u00df catenin signaling deficient conditions as compared to the WT controls. Overall design: Tgfli1:Gal4ubs3;UAS:Kaederk8 embryos were injected at the single cell stage with Morpholinos targeting gpr124  reck  or wnt7aa. Prior to CNS vascular invasion 30 hpf  PHBC endothelial cells expressing the Kaede fluorescent protein  were photoconverted shifting green towards red fluorescence by exposere to a 405 nm laser nanobeam  specifically at the level of the PHBC. Subsequent embryo dissociation and FACS allowed for isolation of PHBC endothelial cells. RNA extraction and sequencing was performed on 4 samples per condition  each containing photoconverted PHBC endothelial cells of 80 embryos.", null, "pubmed:38570687", null, "PHBC endothelial cells 30 hpf  gpr124 MO 2", "GSM7429327", null, "source name:Vascular endothelium|tissue:Vascular endothelium|cell line:PHBC endothelial cells|Stage:30 hpf|cell type:Endothelial cells|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8|genotype:gpr124 MO|treatment:photoconverted|geo loc name:missing|collection date:missing", "PHBC endothelial cells 30 hpf  gpr124 MO 2", "The resulting raw reads were assessed for quality  adapter content  and duplication rates with FastQC. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. 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\u2014outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package84. 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. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers activities at the Universal Protein Resource UniProt. Assembly: DanRer10 Supplementary files format and content: library size normlized counts", "Vascular endothelium", null, "RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250\u2013500\u2009pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.", null, "tissue:Vascular endothelium|cell line:PHBC endothelial cells|Stage:30 hpf|cell type:Endothelial cells|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8|genotype:gpr124 MO|treatment:photoconverted", "GSM7429327", "GSM7429327: PHBC endothelial cells 30 hpf  gpr124 MO 2; Danio rerio; RNA Seq", "GSM7429327 r1", "GSM7429327", "1", "RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250\u2013500\u2009pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP439616", null, "loader:fastq load.py", "C2_MO_gpr124_R1.fastq.gz C2_MO_gpr124_R2.fastq.gz", "fastq fastq", 2095742074.0, 14058965.0, "GSM7429327 r1", null, "A:525622879;C:516816905;G:520123702;T:532027251;N:1151337", null, null, null, null, 525622879, 516816905, 520123702, 532027251, 1151337, "SRX20518069", "SRS17828025", "SRA1644604", "MPI for heart and lung research", "MPI for heart and lung research", 2, 0.88042, 0.88475, 0.10515, 0.10178, 0.81245, 0.81759, 0.54948, 0.54823, 75, 74, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2023-05-25", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [75625, "SRR24740786", "SRX20518068", "SRS17828024", "SRP439616", "PRJNA976345", "An organ specific angiogenic control mechanism for endothelial tailoring", "GSE233488", "Transcriptome Analysis", "To address the role of endothelial Wnt/\u00df catenin signaling in CNS angiogenesis  we compared the bulk transcriptomes of WT and Wnt/\u00df catenin signaling deficient PHBC endothelial cells  prior to CNS vascular invasion. To this end  we used three approaches to abrogate endothelial Wnt/\u00df catenin signaling: Morpholino mediated knock down of gpr124  reck or wnt7aa. We find that the expression of mmp25b is decreased in PHBC endothelial cells of all Wnt/\u00df catenin signaling deficient conditions as compared to the WT controls. Overall design: Tgfli1:Gal4ubs3;UAS:Kaederk8 embryos were injected at the single cell stage with Morpholinos targeting gpr124  reck  or wnt7aa. Prior to CNS vascular invasion 30 hpf  PHBC endothelial cells expressing the Kaede fluorescent protein  were photoconverted shifting green towards red fluorescence by exposere to a 405 nm laser nanobeam  specifically at the level of the PHBC. Subsequent embryo dissociation and FACS allowed for isolation of PHBC endothelial cells. RNA extraction and sequencing was performed on 4 samples per condition  each containing photoconverted PHBC endothelial cells of 80 embryos.", null, "pubmed:38570687", null, "PHBC endothelial cells 30 hpf  gpr124 MO 1", "GSM7429326", null, "source name:Vascular endothelium|tissue:Vascular endothelium|cell line:PHBC endothelial cells|Stage:30 hpf|cell type:Endothelial cells|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8|genotype:gpr124 MO|treatment:photoconverted|geo loc name:missing|collection date:missing", "PHBC endothelial cells 30 hpf  gpr124 MO 1", "The resulting raw reads were assessed for quality  adapter content  and duplication rates with FastQC. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. 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\u2014outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package84. 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. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers activities at the Universal Protein Resource UniProt. Assembly: DanRer10 Supplementary files format and content: library size normlized counts", "Vascular endothelium", null, "RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250\u2013500\u2009pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.", null, "tissue:Vascular endothelium|cell line:PHBC endothelial cells|Stage:30 hpf|cell type:Endothelial cells|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8|genotype:gpr124 MO|treatment:photoconverted", "GSM7429326", "GSM7429326: PHBC endothelial cells 30 hpf  gpr124 MO 1; Danio rerio; RNA Seq", "GSM7429326 r1", "GSM7429326", "1", "RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250\u2013500\u2009pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP439616", null, "loader:fastq load.py", "C1_MO_gpr124_R1.fastq.gz C1_MO_gpr124_R2.fastq.gz", "fastq fastq", 2767627147.0, 18597154.0, "GSM7429326 r1", null, "A:759461761;C:625145665;G:619178577;T:762309844;N:1531300", null, null, null, null, 759461761, 625145665, 619178577, 762309844, 1531300, "SRX20518068", "SRS17828024", "SRA1644604", "MPI for heart and lung research", "MPI for heart and lung research", 2, 0.67422, 0.67595, 0.085, 0.08394, 0.78817, 0.79119, 0.4915, 0.4887, 75, 73, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2023-05-25", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [75626, "SRR24740787", "SRX20518067", "SRS17828023", "SRP439616", "PRJNA976345", "An organ specific angiogenic control mechanism for endothelial tailoring", "GSE233488", "Transcriptome Analysis", "To address the role of endothelial Wnt/\u00df catenin signaling in CNS angiogenesis  we compared the bulk transcriptomes of WT and Wnt/\u00df catenin signaling deficient PHBC endothelial cells  prior to CNS vascular invasion. To this end  we used three approaches to abrogate endothelial Wnt/\u00df catenin signaling: Morpholino mediated knock down of gpr124  reck or wnt7aa. We find that the expression of mmp25b is decreased in PHBC endothelial cells of all Wnt/\u00df catenin signaling deficient conditions as compared to the WT controls. Overall design: Tgfli1:Gal4ubs3;UAS:Kaederk8 embryos were injected at the single cell stage with Morpholinos targeting gpr124  reck  or wnt7aa. Prior to CNS vascular invasion 30 hpf  PHBC endothelial cells expressing the Kaede fluorescent protein  were photoconverted shifting green towards red fluorescence by exposere to a 405 nm laser nanobeam  specifically at the level of the PHBC. Subsequent embryo dissociation and FACS allowed for isolation of PHBC endothelial cells. RNA extraction and sequencing was performed on 4 samples per condition  each containing photoconverted PHBC endothelial cells of 80 embryos.", null, "pubmed:38570687", null, "PHBC endothelial cells 30 hpf  WT 4", "GSM7429325", null, "source name:Vascular endothelium|tissue:Vascular endothelium|cell line:PHBC endothelial cells|Stage:30 hpf|cell type:Endothelial cells|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8|genotype:WT|treatment:photoconverted|geo loc name:missing|collection date:missing", "PHBC endothelial cells 30 hpf  WT 4", "The resulting raw reads were assessed for quality  adapter content  and duplication rates with FastQC. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. 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\u2014outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package84. 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. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers activities at the Universal Protein Resource UniProt. Assembly: DanRer10 Supplementary files format and content: library size normlized counts", "Vascular endothelium", null, "RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250\u2013500\u2009pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.", null, "tissue:Vascular endothelium|cell line:PHBC endothelial cells|Stage:30 hpf|cell type:Endothelial cells|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8|genotype:WT|treatment:photoconverted", "GSM7429325", "GSM7429325: PHBC endothelial cells 30 hpf  WT 4; Danio rerio; RNA Seq", "GSM7429325 r1", "GSM7429325", "1", "RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250\u2013500\u2009pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP439616", null, "loader:fastq load.py", "B4_WT_R1.fastq.gz B4_WT_R2.fastq.gz", "fastq fastq", 2924689332.0, 19639070.0, "GSM7429325 r1", null, "A:809211667;C:649768099;G:647294872;T:816789532;N:1625162", null, null, null, null, 809211667, 649768099, 647294872, 816789532, 1625162, "SRX20518067", "SRS17828023", "SRA1644604", "MPI for heart and lung research", "MPI for heart and lung research", 2, 0.90556, 0.90777, 0.20579, 0.20449, 0.76836, 0.77234, 0.55234, 0.55251, 74, 71, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2023-05-25", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [75627, "SRR24740788", "SRX20518066", "SRS17828022", "SRP439616", "PRJNA976345", "An organ specific angiogenic control mechanism for endothelial tailoring", "GSE233488", "Transcriptome Analysis", "To address the role of endothelial Wnt/\u00df catenin signaling in CNS angiogenesis  we compared the bulk transcriptomes of WT and Wnt/\u00df catenin signaling deficient PHBC endothelial cells  prior to CNS vascular invasion. To this end  we used three approaches to abrogate endothelial Wnt/\u00df catenin signaling: Morpholino mediated knock down of gpr124  reck or wnt7aa. We find that the expression of mmp25b is decreased in PHBC endothelial cells of all Wnt/\u00df catenin signaling deficient conditions as compared to the WT controls. Overall design: Tgfli1:Gal4ubs3;UAS:Kaederk8 embryos were injected at the single cell stage with Morpholinos targeting gpr124  reck  or wnt7aa. Prior to CNS vascular invasion 30 hpf  PHBC endothelial cells expressing the Kaede fluorescent protein  were photoconverted shifting green towards red fluorescence by exposere to a 405 nm laser nanobeam  specifically at the level of the PHBC. Subsequent embryo dissociation and FACS allowed for isolation of PHBC endothelial cells. RNA extraction and sequencing was performed on 4 samples per condition  each containing photoconverted PHBC endothelial cells of 80 embryos.", null, "pubmed:38570687", null, "PHBC endothelial cells 30 hpf  WT 3", "GSM7429324", null, "source name:Vascular endothelium|tissue:Vascular endothelium|cell line:PHBC endothelial cells|Stage:30 hpf|cell type:Endothelial cells|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8|genotype:WT|treatment:photoconverted|geo loc name:missing|collection date:missing", "PHBC endothelial cells 30 hpf  WT 3", "The resulting raw reads were assessed for quality  adapter content  and duplication rates with FastQC. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. 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\u2014outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package84. 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. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers activities at the Universal Protein Resource UniProt. Assembly: DanRer10 Supplementary files format and content: library size normlized counts", "Vascular endothelium", null, "RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250\u2013500\u2009pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.", null, "tissue:Vascular endothelium|cell line:PHBC endothelial cells|Stage:30 hpf|cell type:Endothelial cells|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8|genotype:WT|treatment:photoconverted", "GSM7429324", "GSM7429324: PHBC endothelial cells 30 hpf  WT 3; Danio rerio; RNA Seq", "GSM7429324 r1", "GSM7429324", "1", "RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250\u2013500\u2009pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP439616", null, "loader:fastq load.py", "B3_WT_R1.fastq.gz B3_WT_R2.fastq.gz", "fastq fastq", 2556876101.0, 17158306.0, "GSM7429324 r1", null, "A:674099968;C:605785858;G:602757969;T:672809126;N:1423180", null, null, null, null, 674099968, 605785858, 602757969, 672809126, 1423180, "SRX20518066", "SRS17828022", "SRA1644604", "MPI for heart and lung research", "MPI for heart and lung research", 2, 0.93764, 0.93809, 0.09995, 0.09895, 0.76976, 0.77181, 0.47357, 0.47232, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2023-05-25", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [75628, "SRR24740789", "SRX20518065", "SRS17828021", "SRP439616", "PRJNA976345", "An organ specific angiogenic control mechanism for endothelial tailoring", "GSE233488", "Transcriptome Analysis", "To address the role of endothelial Wnt/\u00df catenin signaling in CNS angiogenesis  we compared the bulk transcriptomes of WT and Wnt/\u00df catenin signaling deficient PHBC endothelial cells  prior to CNS vascular invasion. To this end  we used three approaches to abrogate endothelial Wnt/\u00df catenin signaling: Morpholino mediated knock down of gpr124  reck or wnt7aa. We find that the expression of mmp25b is decreased in PHBC endothelial cells of all Wnt/\u00df catenin signaling deficient conditions as compared to the WT controls. Overall design: Tgfli1:Gal4ubs3;UAS:Kaederk8 embryos were injected at the single cell stage with Morpholinos targeting gpr124  reck  or wnt7aa. Prior to CNS vascular invasion 30 hpf  PHBC endothelial cells expressing the Kaede fluorescent protein  were photoconverted shifting green towards red fluorescence by exposere to a 405 nm laser nanobeam  specifically at the level of the PHBC. Subsequent embryo dissociation and FACS allowed for isolation of PHBC endothelial cells. RNA extraction and sequencing was performed on 4 samples per condition  each containing photoconverted PHBC endothelial cells of 80 embryos.", null, "pubmed:38570687", null, "PHBC endothelial cells 30 hpf  WT 2", "GSM7429323", null, "source name:Vascular endothelium|tissue:Vascular endothelium|cell line:PHBC endothelial cells|Stage:30 hpf|cell type:Endothelial cells|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8|genotype:WT|treatment:photoconverted|geo loc name:missing|collection date:missing", "PHBC endothelial cells 30 hpf  WT 2", "The resulting raw reads were assessed for quality  adapter content  and duplication rates with FastQC. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. 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\u2014outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package84. 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. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers activities at the Universal Protein Resource UniProt. Assembly: DanRer10 Supplementary files format and content: library size normlized counts", "Vascular endothelium", null, "RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250\u2013500\u2009pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.", null, "tissue:Vascular endothelium|cell line:PHBC endothelial cells|Stage:30 hpf|cell type:Endothelial cells|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8|genotype:WT|treatment:photoconverted", "GSM7429323", "GSM7429323: PHBC endothelial cells 30 hpf  WT 2; Danio rerio; RNA Seq", "GSM7429323 r1", "GSM7429323", "1", "RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250\u2013500\u2009pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP439616", null, "loader:fastq load.py", "B2_WT_R1.fastq.gz B2_WT_R2.fastq.gz", "fastq fastq", 2719619180.0, 18253304.0, "GSM7429323 r1", null, "A:737514407;C:623462360;G:618552838;T:738582283;N:1507292", null, null, null, null, 737514407, 623462360, 618552838, 738582283, 1507292, "SRX20518065", "SRS17828021", "SRA1644604", "MPI for heart and lung research", "MPI for heart and lung research", 2, 0.92769, 0.92835, 0.12021, 0.11953, 0.74852, 0.75116, 0.48883, 0.49108, 75, 74, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2023-05-25", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [75629, "SRR24740790", "SRX20518064", "SRS17828020", "SRP439616", "PRJNA976345", "An organ specific angiogenic control mechanism for endothelial tailoring", "GSE233488", "Transcriptome Analysis", "To address the role of endothelial Wnt/\u00df catenin signaling in CNS angiogenesis  we compared the bulk transcriptomes of WT and Wnt/\u00df catenin signaling deficient PHBC endothelial cells  prior to CNS vascular invasion. To this end  we used three approaches to abrogate endothelial Wnt/\u00df catenin signaling: Morpholino mediated knock down of gpr124  reck or wnt7aa. We find that the expression of mmp25b is decreased in PHBC endothelial cells of all Wnt/\u00df catenin signaling deficient conditions as compared to the WT controls. Overall design: Tgfli1:Gal4ubs3;UAS:Kaederk8 embryos were injected at the single cell stage with Morpholinos targeting gpr124  reck  or wnt7aa. Prior to CNS vascular invasion 30 hpf  PHBC endothelial cells expressing the Kaede fluorescent protein  were photoconverted shifting green towards red fluorescence by exposere to a 405 nm laser nanobeam  specifically at the level of the PHBC. Subsequent embryo dissociation and FACS allowed for isolation of PHBC endothelial cells. RNA extraction and sequencing was performed on 4 samples per condition  each containing photoconverted PHBC endothelial cells of 80 embryos.", null, "pubmed:38570687", null, "PHBC endothelial cells 30 hpf  WT 1", "GSM7429322", null, "source name:Vascular endothelium|tissue:Vascular endothelium|cell line:PHBC endothelial cells|Stage:30 hpf|cell type:Endothelial cells|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8|genotype:WT|treatment:photoconverted|geo loc name:missing|collection date:missing", "PHBC endothelial cells 30 hpf  WT 1", "The resulting raw reads were assessed for quality  adapter content  and duplication rates with FastQC. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. 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\u2014outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package84. 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. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers activities at the Universal Protein Resource UniProt. Assembly: DanRer10 Supplementary files format and content: library size normlized counts", "Vascular endothelium", null, "RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250\u2013500\u2009pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.", null, "tissue:Vascular endothelium|cell line:PHBC endothelial cells|Stage:30 hpf|cell type:Endothelial cells|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8|genotype:WT|treatment:photoconverted", "GSM7429322", "GSM7429322: PHBC endothelial cells 30 hpf  WT 1; Danio rerio; RNA Seq", "GSM7429322 r1", "GSM7429322", "1", "RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250\u2013500\u2009pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP439616", null, "loader:fastq load.py", "B1_WT_R1.fastq.gz B1_WT_R2.fastq.gz", "fastq fastq", 3264716585.0, 21921700.0, "GSM7429322 r1", null, "A:879625441;C:754137197;G:748183608;T:880983333;N:1787006", null, null, null, null, 879625441, 754137197, 748183608, 880983333, 1787006, "SRX20518064", "SRS17828020", "SRA1644604", "MPI for heart and lung research", "MPI for heart and lung research", 2, 0.82107, 0.82113, 0.12446, 0.12391, 0.78007, 0.7847, 0.48973, 0.48394, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2023-05-25", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [75630, "SRR24740791", "SRX20518063", "SRS17828019", "SRP439616", "PRJNA976345", "An organ specific angiogenic control mechanism for endothelial tailoring", "GSE233488", "Transcriptome Analysis", "To address the role of endothelial Wnt/\u00df catenin signaling in CNS angiogenesis  we compared the bulk transcriptomes of WT and Wnt/\u00df catenin signaling deficient PHBC endothelial cells  prior to CNS vascular invasion. To this end  we used three approaches to abrogate endothelial Wnt/\u00df catenin signaling: Morpholino mediated knock down of gpr124  reck or wnt7aa. We find that the expression of mmp25b is decreased in PHBC endothelial cells of all Wnt/\u00df catenin signaling deficient conditions as compared to the WT controls. Overall design: Tgfli1:Gal4ubs3;UAS:Kaederk8 embryos were injected at the single cell stage with Morpholinos targeting gpr124  reck  or wnt7aa. Prior to CNS vascular invasion 30 hpf  PHBC endothelial cells expressing the Kaede fluorescent protein  were photoconverted shifting green towards red fluorescence by exposere to a 405 nm laser nanobeam  specifically at the level of the PHBC. Subsequent embryo dissociation and FACS allowed for isolation of PHBC endothelial cells. RNA extraction and sequencing was performed on 4 samples per condition  each containing photoconverted PHBC endothelial cells of 80 embryos.", null, "pubmed:38570687", null, "Endothelial cells 30 hpf  negative 3", "GSM7429321", null, "source name:Vascular endothelium|tissue:Vascular endothelium|cell line:Endothelial cells|Stage:30 hpf|cell type:Endothelial cells|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8|genotype:WT|treatment:Non photoconverted|geo loc name:missing|collection date:missing", "Endothelial cells 30 hpf  negative 3", "The resulting raw reads were assessed for quality  adapter content  and duplication rates with FastQC. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. 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\u2014outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package84. 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. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers activities at the Universal Protein Resource UniProt. Assembly: DanRer10 Supplementary files format and content: library size normlized counts", "Vascular endothelium", null, "RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250\u2013500\u2009pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.", null, "tissue:Vascular endothelium|cell line:Endothelial cells|Stage:30 hpf|cell type:Endothelial cells|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8|genotype:WT|treatment:Non photoconverted", "GSM7429321", "GSM7429321: Endothelial cells 30 hpf  negative 3; Danio rerio; RNA Seq", "GSM7429321 r1", "GSM7429321", "1", "RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250\u2013500\u2009pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP439616", null, "loader:fastq load.py", "A3_Neg_controls_R1.fastq.gz A3_Neg_controls_R2.fastq.gz", "fastq fastq", 2754470229.0, 18487768.0, "GSM7429321 r1", null, "A:707439749;C:673922384;G:669885592;T:701717257;N:1505247", null, null, null, null, 707439749, 673922384, 669885592, 701717257, 1505247, "SRX20518063", "SRS17828019", "SRA1644604", "MPI for heart and lung research", "MPI for heart and lung research", 2, 0.95585, 0.9557, 0.05025, 0.04999, 0.7837, 0.78693, 0.40771, 0.40943, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2023-05-25", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [75631, "SRR24740792", "SRX20518062", "SRS17828018", "SRP439616", "PRJNA976345", "An organ specific angiogenic control mechanism for endothelial tailoring", "GSE233488", "Transcriptome Analysis", "To address the role of endothelial Wnt/\u00df catenin signaling in CNS angiogenesis  we compared the bulk transcriptomes of WT and Wnt/\u00df catenin signaling deficient PHBC endothelial cells  prior to CNS vascular invasion. To this end  we used three approaches to abrogate endothelial Wnt/\u00df catenin signaling: Morpholino mediated knock down of gpr124  reck or wnt7aa. We find that the expression of mmp25b is decreased in PHBC endothelial cells of all Wnt/\u00df catenin signaling deficient conditions as compared to the WT controls. Overall design: Tgfli1:Gal4ubs3;UAS:Kaederk8 embryos were injected at the single cell stage with Morpholinos targeting gpr124  reck  or wnt7aa. Prior to CNS vascular invasion 30 hpf  PHBC endothelial cells expressing the Kaede fluorescent protein  were photoconverted shifting green towards red fluorescence by exposere to a 405 nm laser nanobeam  specifically at the level of the PHBC. Subsequent embryo dissociation and FACS allowed for isolation of PHBC endothelial cells. RNA extraction and sequencing was performed on 4 samples per condition  each containing photoconverted PHBC endothelial cells of 80 embryos.", null, "pubmed:38570687", null, "Endothelial cells 30 hpf  negative 2", "GSM7429320", null, "source name:Vascular endothelium|tissue:Vascular endothelium|cell line:Endothelial cells|Stage:30 hpf|cell type:Endothelial cells|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8|genotype:WT|treatment:Non photoconverted|geo loc name:missing|collection date:missing", "Endothelial cells 30 hpf  negative 2", "The resulting raw reads were assessed for quality  adapter content  and duplication rates with FastQC. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. 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\u2014outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package84. 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. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers activities at the Universal Protein Resource UniProt. Assembly: DanRer10 Supplementary files format and content: library size normlized counts", "Vascular endothelium", null, "RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250\u2013500\u2009pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.", null, "tissue:Vascular endothelium|cell line:Endothelial cells|Stage:30 hpf|cell type:Endothelial cells|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8|genotype:WT|treatment:Non photoconverted", "GSM7429320", "GSM7429320: Endothelial cells 30 hpf  negative 2; Danio rerio; RNA Seq", "GSM7429320 r1", "GSM7429320", "1", "RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250\u2013500\u2009pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP439616", null, "loader:fastq load.py", "A2_Neg_controls_R1.fastq.gz A2_Neg_controls_R2.fastq.gz", "fastq fastq", 2820835655.0, 18927799.0, "GSM7429320 r1", null, "A:731665823;C:680271247;G:678251388;T:729095004;N:1552193", null, null, null, null, 731665823, 680271247, 678251388, 729095004, 1552193, "SRX20518062", "SRS17828018", "SRA1644604", "MPI for heart and lung research", "MPI for heart and lung research", 2, 0.92704, 0.92685, 0.08579, 0.0849, 0.78597, 0.79091, 0.45975, 0.46663, 74, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2023-05-25", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [75632, "SRR24740793", "SRX20518061", "SRS17828017", "SRP439616", "PRJNA976345", "An organ specific angiogenic control mechanism for endothelial tailoring", "GSE233488", "Transcriptome Analysis", "To address the role of endothelial Wnt/\u00df catenin signaling in CNS angiogenesis  we compared the bulk transcriptomes of WT and Wnt/\u00df catenin signaling deficient PHBC endothelial cells  prior to CNS vascular invasion. To this end  we used three approaches to abrogate endothelial Wnt/\u00df catenin signaling: Morpholino mediated knock down of gpr124  reck or wnt7aa. We find that the expression of mmp25b is decreased in PHBC endothelial cells of all Wnt/\u00df catenin signaling deficient conditions as compared to the WT controls. Overall design: Tgfli1:Gal4ubs3;UAS:Kaederk8 embryos were injected at the single cell stage with Morpholinos targeting gpr124  reck  or wnt7aa. Prior to CNS vascular invasion 30 hpf  PHBC endothelial cells expressing the Kaede fluorescent protein  were photoconverted shifting green towards red fluorescence by exposere to a 405 nm laser nanobeam  specifically at the level of the PHBC. Subsequent embryo dissociation and FACS allowed for isolation of PHBC endothelial cells. RNA extraction and sequencing was performed on 4 samples per condition  each containing photoconverted PHBC endothelial cells of 80 embryos.", null, "pubmed:38570687", null, "Endothelial cells 30 hpf  negative 1", "GSM7429319", null, "source name:Vascular endothelium|tissue:Vascular endothelium|cell line:Endothelial cells|Stage:30 hpf|cell type:Endothelial cells|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8|genotype:WT|treatment:Non photoconverted|geo loc name:missing|collection date:missing", "Endothelial cells 30 hpf  negative 1", "The resulting raw reads were assessed for quality  adapter content  and duplication rates with FastQC. Trimmomatic version 0.33 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. 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\u2014outFilterMismatchNoverLmax 0.1\u201d to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package84. 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. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers activities at the Universal Protein Resource UniProt. Assembly: DanRer10 Supplementary files format and content: library size normlized counts", "Vascular endothelium", null, "RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250\u2013500\u2009pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.", null, "tissue:Vascular endothelium|cell line:Endothelial cells|Stage:30 hpf|cell type:Endothelial cells|transgene:Tgfli1:Gal4ubs3;UAS:Kaederk8|genotype:WT|treatment:Non photoconverted", "GSM7429319", "GSM7429319: Endothelial cells 30 hpf  negative 1; Danio rerio; RNA Seq", "GSM7429319 r1", "GSM7429319", "1", "RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set  Qiagen to avoid contamination by genomic DNA. RNA amount was adjusted on number of isolated cells by FACS and 250\u2013500\u2009pg total RNA was used as input for SMART Seq\u00ae v4 Ultra\u00ae Low Input RNA Kit Takara Bio for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Bio.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP439616", null, "loader:fastq load.py", "A1_Neg_controls_R1.fastq.gz A1_Neg_controls_R2.fastq.gz", "fastq fastq", 3578902225.0, 24014303.0, "GSM7429319 r1", null, "A:937280207;C:855762487;G:851738460;T:932155139;N:1965932", null, null, null, null, 937280207, 855762487, 851738460, 932155139, 1965932, "SRX20518061", "SRS17828017", "SRA1644604", "MPI for heart and lung research", "MPI for heart and lung research", 2, 0.95371, 0.95422, 0.08678, 0.08593, 0.7709, 0.77364, 0.46937, 0.46998, 75, 75, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Germany", "2023-05-25", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"]], "truncated": false, "filtered_table_rows_count": 35, "expanded_columns": [], 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