rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse 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,,pubmed:35199829,,Smartseq2 AXL E3 endo Danio,GSM4432625,,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,,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°C 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°C 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’ scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010.,,strain:flk:GFP|cell tye:endothelial cells,GSM4432625,GSM4432625: Smartseq2 AXL E3 endo Danio; Danio rerio; RNA Seq,GSM4432625,,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°C 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°C 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:GSM4432625,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP254020,,,AXL-E3_HHVK7CCXY_L3_1.clean.fq.gz AXL-E3_HHVK7CCXY_L3_2.clean.fq.gz,fastq fastq,1568068200.0,5226894.0,GSM4432625 r1,0:150 1:150,A:437547051;C:305827667;G:317225931;T:507380843;N:86708,150,150,,,437547051,305827667,317225931,507380843,86708,SRX7998914,SRS6376277,SRA1059261,GEO,"Chen & Liu Lab, State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University., Sichuan University",2,0.90556,0.91298,0.73969,0.74743,0.94888,0.95061,0.47195,0.48203,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,China,2020-03-25,Larval,Larval,Endothelium,Cardiovascular System 58568,SRR11420477,SRX7998913,SRS6376276,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,,pubmed:35199829,,Smartseq2 AXL E2 endo Danio,GSM4432624,,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,,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°C 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°C 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’ scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010.,,strain:flk:GFP|cell tye:endothelial cells,GSM4432624,GSM4432624: Smartseq2 AXL E2 endo Danio; Danio rerio; RNA Seq,GSM4432624,,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°C 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°C 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:GSM4432624,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP254020,,,AXL-E2_HHVK7CCXY_L3_2.clean.fq.gz AXL-E2_HHVK7CCXY_L3_1.clean.fq.gz,fastq fastq,1506462600.0,5021542.0,GSM4432624 r1,0:150 1:150,A:419138482;C:294375706;G:306403925;T:486460081;N:84406,150,150,,,419138482,294375706,306403925,486460081,84406,SRX7998913,SRS6376276,SRA1059261,GEO,"Chen & Liu Lab, State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University., Sichuan University",2,0.90958,0.91859,0.78806,0.79513,0.96327,0.96477,0.45808,0.46876,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,China,2020-03-25,Larval,Larval,Endothelium,Cardiovascular System 58569,SRR11420476,SRX7998912,SRS6376275,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,,pubmed:35199829,,Smartseq2 AXL E1 endo Danio,GSM4432623,,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,,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°C 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°C 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’ scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010.,,strain:flk:GFP|cell tye:endothelial cells,GSM4432623,GSM4432623: Smartseq2 AXL E1 endo Danio; Danio rerio; RNA Seq,GSM4432623,,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°C 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°C 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:GSM4432623,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP254020,,,AXL-E1_HHVK7CCXY_L3_1.clean.fq.gz AXL-E1_HHVK7CCXY_L3_2.clean.fq.gz,fastq fastq,1583815800.0,5279386.0,GSM4432623 r1,0:150 1:150,A:440756401;C:310619619;G:322228450;T:510122285;N:89045,150,150,,,440756401,310619619,322228450,510122285,89045,SRX7998912,SRS6376275,SRA1059261,GEO,"Chen & Liu Lab, State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University., Sichuan University",2,0.91047,0.91678,0.69764,0.70328,0.95217,0.95349,0.46044,0.44698,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,China,2020-03-25,Larval,Larval,Endothelium,Cardiovascular System 58570,SRR11420475,SRX7998911,SRS6376274,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,,pubmed:35199829,,Smartseq2 AXL D3 endo Danio,GSM4432622,,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,,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°C 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°C 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’ scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010.,,strain:flk:GFP|cell tye:endothelial cells,GSM4432622,GSM4432622: Smartseq2 AXL D3 endo Danio; Danio rerio; RNA Seq,GSM4432622,,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°C 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°C 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:GSM4432622,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP254020,,,AXL-D3_HHVK7CCXY_L3_1.clean.fq.gz AXL-D3_HHVK7CCXY_L3_2.clean.fq.gz,fastq fastq,1602725100.0,5342417.0,GSM4432622 r1,0:150 1:150,A:454250175;C:320141617;G:330588624;T:497655411;N:89273,150,150,,,454250175,320141617,330588624,497655411,89273,SRX7998911,SRS6376274,SRA1059261,GEO,"Chen & Liu Lab, State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University., Sichuan University",2,0.82435,0.83275,0.22763,0.23084,0.88716,0.89023,0.75529,0.75251,150,150,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,China,2020-03-25,Larval,Larval,Endothelium,Cardiovascular System 58571,SRR11420474,SRX7998910,SRS6376273,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,,pubmed:35199829,,Smartseq2 AXL C3 endo Danio,GSM4432621,,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,,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°C 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°C 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’ scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010.,,strain:flk:GFP|cell tye:endothelial cells,GSM4432621,GSM4432621: Smartseq2 AXL C3 endo Danio; Danio rerio; RNA Seq,GSM4432621,,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°C 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°C 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,,SRP254020,,,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,,,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,,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,,pubmed:35199829,,Smartseq2 AXL C2 endo Danio,GSM4432620,,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,,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°C 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°C 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’ scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010.,,strain:flk:GFP|cell tye:endothelial cells,GSM4432620,GSM4432620: Smartseq2 AXL C2 endo Danio; Danio rerio; RNA Seq,GSM4432620,,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°C 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°C 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,,SRP254020,,,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,,,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,,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,,pubmed:35199829,,Smartseq2 AXL C1 endo Danio,GSM4432619,,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,,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°C 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°C 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’ scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010.,,strain:flk:GFP|cell tye:endothelial cells,GSM4432619,GSM4432619: Smartseq2 AXL C1 endo Danio; Danio rerio; RNA Seq,GSM4432619,,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°C 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°C 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,,SRP254020,,,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,,,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,,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,,pubmed:35199829,,Smartseq2 AXL B2 endo Danio,GSM4432618,,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,,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°C 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°C 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’ scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010.,,strain:flk:GFP|cell tye:endothelial cells,GSM4432618,GSM4432618: Smartseq2 AXL B2 endo Danio; Danio rerio; RNA Seq,GSM4432618,,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°C 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°C 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,,SRP254020,,,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,,,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,,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,,pubmed:35199829,,Smartseq2 AXL B1 endo Danio,GSM4432617,,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,,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°C 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°C 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’ scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010.,,strain:flk:GFP|cell tye:endothelial cells,GSM4432617,GSM4432617: Smartseq2 AXL B1 endo Danio; Danio rerio; RNA Seq,GSM4432617,,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°C 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°C 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,,SRP254020,,,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,,,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,,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,,pubmed:35199829,,Smartseq2 AXL A3 endo Danio,GSM4432616,,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,,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°C 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°C 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’ scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010.,,strain:flk:GFP|cell tye:endothelial cells,GSM4432616,GSM4432616: Smartseq2 AXL A3 endo Danio; Danio rerio; RNA Seq,GSM4432616,,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°C 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°C 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,,SRP254020,,,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,,,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,,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,,pubmed:35199829,,Smartseq2 AXL A2 endo Danio,GSM4432615,,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,,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°C 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°C 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’ scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010.,,strain:flk:GFP|cell tye:endothelial cells,GSM4432615,GSM4432615: Smartseq2 AXL A2 endo Danio; Danio rerio; RNA Seq,GSM4432615,,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°C 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°C 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,,SRP254020,,,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,,,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,,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,,pubmed:35199829,,Smartseq2 AXL A1 endo Danio,GSM4432614,,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,,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°C 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°C 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’ scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang 2010.,,strain:flk:GFP|cell tye:endothelial cells,GSM4432614,GSM4432614: Smartseq2 AXL A1 endo Danio; Danio rerio; RNA Seq,GSM4432614,,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°C 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°C 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,,SRP254020,,,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,,,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,,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/ß catenin signaling in CNS angiogenesis we compared the bulk transcriptomes of WT and Wnt/ß catenin signaling deficient PHBC endothelial cells prior to CNS vascular invasion. To this end we used three approaches to abrogate endothelial Wnt/ß 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/ß 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.,,pubmed:38570687,,PHBC endothelial cells 30 hpf wnt7aa MO 4,GSM7429341,,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 “—outFilterMismatchNoverLmax 0.1” 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,,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 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® 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.,,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 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® 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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP439616,,loader:fastq load.py,F4_MO_wnt7aa_R1.fastq.gz F4_MO_wnt7aa_R2.fastq.gz,fastq fastq,3410657071.0,22888059.0,GSM7429341 r1,,A:930255790;C:774998735;G:770566602;T:932969311;N:1866633,,,,,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,,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/ß catenin signaling in CNS angiogenesis we compared the bulk transcriptomes of WT and Wnt/ß catenin signaling deficient PHBC endothelial cells prior to CNS vascular invasion. To this end we used three approaches to abrogate endothelial Wnt/ß 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/ß 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.,,pubmed:38570687,,PHBC endothelial cells 30 hpf wnt7aa MO 3,GSM7429340,,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 “—outFilterMismatchNoverLmax 0.1” 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,,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 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® 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.,,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 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® 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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP439616,,loader:fastq load.py,F3_MO_wnt7aa_R1.fastq.gz F3_MO_wnt7aa_R2.fastq.gz,fastq fastq,2844102685.0,19087245.0,GSM7429340 r1,,A:753836724;C:664365246;G:664895731;T:759443497;N:1561487,,,,,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,,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/ß catenin signaling in CNS angiogenesis we compared the bulk transcriptomes of WT and Wnt/ß catenin signaling deficient PHBC endothelial cells prior to CNS vascular invasion. To this end we used three approaches to abrogate endothelial Wnt/ß 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/ß 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.,,pubmed:38570687,,PHBC endothelial cells 30 hpf wnt7aa MO 2,GSM7429339,,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 “—outFilterMismatchNoverLmax 0.1” 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,,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 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® 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.,,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 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® 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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP439616,,loader:fastq load.py,F2_MO_wnt7aa_R1.fastq.gz F2_MO_wnt7aa_R2.fastq.gz,fastq fastq,3003877741.0,20155237.0,GSM7429339 r1,,A:806731621;C:691626094;G:690105872;T:813757253;N:1656901,,,,,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,,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/ß catenin signaling in CNS angiogenesis we compared the bulk transcriptomes of WT and Wnt/ß catenin signaling deficient PHBC endothelial cells prior to CNS vascular invasion. To this end we used three approaches to abrogate endothelial Wnt/ß 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/ß 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.,,pubmed:38570687,,PHBC endothelial cells 30 hpf wnt7aa MO 1,GSM7429338,,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 “—outFilterMismatchNoverLmax 0.1” 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,,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 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® 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.,,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 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® 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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP439616,,loader:fastq load.py,F1_MO_wnt7aa_R1.fastq.gz F1_MO_wnt7aa_R2.fastq.gz,fastq fastq,2134056620.0,14319615.0,GSM7429338 r1,,A:574764769;C:489478372;G:488808981;T:579820041;N:1184457,,,,,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,,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/ß catenin signaling in CNS angiogenesis we compared the bulk transcriptomes of WT and Wnt/ß catenin signaling deficient PHBC endothelial cells prior to CNS vascular invasion. To this end we used three approaches to abrogate endothelial Wnt/ß 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/ß 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.,,pubmed:38570687,,PHBC endothelial cells 30 hpf reck MO 4,GSM7429337,,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 “—outFilterMismatchNoverLmax 0.1” 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,,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 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® 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.,,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 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® 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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP439616,,loader:fastq load.py,E4_MO_reck_R1.fastq.gz E4_MO_reck_R2.fastq.gz,fastq fastq,2600213337.0,17457111.0,GSM7429337 r1,,A:711797268;C:588127202;G:584757641;T:714124587;N:1406639,,,,,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,,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/ß catenin signaling in CNS angiogenesis we compared the bulk transcriptomes of WT and Wnt/ß catenin signaling deficient PHBC endothelial cells prior to CNS vascular invasion. To this end we used three approaches to abrogate endothelial Wnt/ß 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/ß 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.,,pubmed:38570687,,PHBC endothelial cells 30 hpf reck MO 3,GSM7429336,,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 “—outFilterMismatchNoverLmax 0.1” 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,,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 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® 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.,,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 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® 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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP439616,,loader:fastq load.py,E3_MO_reck_R1.fastq.gz E3_MO_reck_R2.fastq.gz,fastq fastq,1741572044.0,11687076.0,GSM7429336 r1,,A:472997022;C:397732899;G:395569364;T:474320408;N:952351,,,,,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,,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/ß catenin signaling in CNS angiogenesis we compared the bulk transcriptomes of WT and Wnt/ß catenin signaling deficient PHBC endothelial cells prior to CNS vascular invasion. To this end we used three approaches to abrogate endothelial Wnt/ß 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/ß 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.,,pubmed:38570687,,PHBC endothelial cells 30 hpf reck MO 2,GSM7429335,,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 “—outFilterMismatchNoverLmax 0.1” 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,,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 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® 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.,,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 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® 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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP439616,,loader:fastq load.py,E2_MO_reck_R1.fastq.gz E2_MO_reck_R2.fastq.gz,fastq fastq,2671658198.0,17928556.0,GSM7429335 r1,,A:725812218;C:610551715;G:606842688;T:726993096;N:1458481,,,,,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,,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/ß catenin signaling in CNS angiogenesis we compared the bulk transcriptomes of WT and Wnt/ß catenin signaling deficient PHBC endothelial cells prior to CNS vascular invasion. To this end we used three approaches to abrogate endothelial Wnt/ß 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/ß 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.,,pubmed:38570687,,PHBC endothelial cells 30 hpf reck MO 1,GSM7429334,,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 “—outFilterMismatchNoverLmax 0.1” 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,,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 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® 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.,,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 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® 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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP439616,,loader:fastq load.py,E1_MO_reck_R1.fastq.gz E1_MO_reck_R2.fastq.gz,fastq fastq,2779576944.0,19473447.0,GSM7429334 r1,,A:818491725;C:569735041;G:564250518;T:825468450;N:1631210,,,,,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,,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/ß catenin signaling in CNS angiogenesis we compared the bulk transcriptomes of WT and Wnt/ß catenin signaling deficient PHBC endothelial cells prior to CNS vascular invasion. To this end we used three approaches to abrogate endothelial Wnt/ß 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/ß 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.,,pubmed:38570687,,PHBC endothelial cells 30 hpf TF MO 4,GSM7429333,,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 “—outFilterMismatchNoverLmax 0.1” 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,,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 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® 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.,,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 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® 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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP439616,,loader:fastq load.py,D4_MO_TF_R1.fastq.gz D4_MO_TF_R2.fastq.gz,fastq fastq,3262028321.0,21890211.0,GSM7429333 r1,,A:876880120;C:749366908;G:748032046;T:885943266;N:1805981,,,,,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,,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/ß catenin signaling in CNS angiogenesis we compared the bulk transcriptomes of WT and Wnt/ß catenin signaling deficient PHBC endothelial cells prior to CNS vascular invasion. To this end we used three approaches to abrogate endothelial Wnt/ß 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/ß 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.,,pubmed:38570687,,PHBC endothelial cells 30 hpf TF MO 3,GSM7429332,,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 “—outFilterMismatchNoverLmax 0.1” 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,,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 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® 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.,,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 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® 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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP439616,,loader:fastq load.py,D3_MO_TF_R1.fastq.gz D3_MO_TF_R2.fastq.gz,fastq fastq,911957449.0,6119680.0,GSM7429332 r1,,A:240966620;C:213588458;G:213137469;T:243759752;N:505150,,,,,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,,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/ß catenin signaling in CNS angiogenesis we compared the bulk transcriptomes of WT and Wnt/ß catenin signaling deficient PHBC endothelial cells prior to CNS vascular invasion. To this end we used three approaches to abrogate endothelial Wnt/ß 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/ß 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.,,pubmed:38570687,,PHBC endothelial cells 30 hpf TF MO 2,GSM7429331,,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 “—outFilterMismatchNoverLmax 0.1” 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,,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 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® 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.,,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 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® 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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP439616,,loader:fastq load.py,D2_MO_TF_R1.fastq.gz D2_MO_TF_R2.fastq.gz,fastq fastq,2828207009.0,18989270.0,GSM7429331 r1,,A:742830477;C:672427123;G:669193099;T:742200169;N:1556141,,,,,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,,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/ß catenin signaling in CNS angiogenesis we compared the bulk transcriptomes of WT and Wnt/ß catenin signaling deficient PHBC endothelial cells prior to CNS vascular invasion. To this end we used three approaches to abrogate endothelial Wnt/ß 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/ß 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.,,pubmed:38570687,,PHBC endothelial cells 30 hpf TF MO 1,GSM7429330,,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 “—outFilterMismatchNoverLmax 0.1” 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,,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 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® 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.,,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 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® 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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP439616,,loader:fastq load.py,D1_MO_TF_R1.fastq.gz D1_MO_TF_R2.fastq.gz,fastq fastq,3219964468.0,21606481.0,GSM7429330 r1,,A:865281524;C:741783926;G:739687813;T:871436747;N:1774458,,,,,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,,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/ß catenin signaling in CNS angiogenesis we compared the bulk transcriptomes of WT and Wnt/ß catenin signaling deficient PHBC endothelial cells prior to CNS vascular invasion. To this end we used three approaches to abrogate endothelial Wnt/ß 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/ß 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.,,pubmed:38570687,,PHBC endothelial cells 30 hpf gpr124 MO 4,GSM7429329,,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 “—outFilterMismatchNoverLmax 0.1” 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,,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 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® 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.,,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 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® 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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP439616,,loader:fastq load.py,C4_MO_gpr124_R1.fastq.gz C4_MO_gpr124_R2.fastq.gz,fastq fastq,2735180426.0,18351837.0,GSM7429329 r1,,A:727609254;C:631295729;G:635633455;T:739158077;N:1483911,,,,,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,,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/ß catenin signaling in CNS angiogenesis we compared the bulk transcriptomes of WT and Wnt/ß catenin signaling deficient PHBC endothelial cells prior to CNS vascular invasion. To this end we used three approaches to abrogate endothelial Wnt/ß 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/ß 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.,,pubmed:38570687,,PHBC endothelial cells 30 hpf gpr124 MO 3,GSM7429328,,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 “—outFilterMismatchNoverLmax 0.1” 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,,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 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® 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.,,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 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® 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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP439616,,loader:fastq load.py,C3_MO_gpr124_R1.fastq.gz C3_MO_gpr124_R2.fastq.gz,fastq fastq,2832145279.0,19001125.0,GSM7429328 r1,,A:742506972;C:669366817;G:669405672;T:749307010;N:1558808,,,,,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,,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/ß catenin signaling in CNS angiogenesis we compared the bulk transcriptomes of WT and Wnt/ß catenin signaling deficient PHBC endothelial cells prior to CNS vascular invasion. To this end we used three approaches to abrogate endothelial Wnt/ß 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/ß 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.,,pubmed:38570687,,PHBC endothelial cells 30 hpf gpr124 MO 2,GSM7429327,,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 “—outFilterMismatchNoverLmax 0.1” 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,,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 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® 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.,,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 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® 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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP439616,,loader:fastq load.py,C2_MO_gpr124_R1.fastq.gz C2_MO_gpr124_R2.fastq.gz,fastq fastq,2095742074.0,14058965.0,GSM7429327 r1,,A:525622879;C:516816905;G:520123702;T:532027251;N:1151337,,,,,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,,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/ß catenin signaling in CNS angiogenesis we compared the bulk transcriptomes of WT and Wnt/ß catenin signaling deficient PHBC endothelial cells prior to CNS vascular invasion. To this end we used three approaches to abrogate endothelial Wnt/ß 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/ß 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.,,pubmed:38570687,,PHBC endothelial cells 30 hpf gpr124 MO 1,GSM7429326,,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 “—outFilterMismatchNoverLmax 0.1” 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,,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 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® 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.,,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 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® 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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP439616,,loader:fastq load.py,C1_MO_gpr124_R1.fastq.gz C1_MO_gpr124_R2.fastq.gz,fastq fastq,2767627147.0,18597154.0,GSM7429326 r1,,A:759461761;C:625145665;G:619178577;T:762309844;N:1531300,,,,,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,,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/ß catenin signaling in CNS angiogenesis we compared the bulk transcriptomes of WT and Wnt/ß catenin signaling deficient PHBC endothelial cells prior to CNS vascular invasion. To this end we used three approaches to abrogate endothelial Wnt/ß 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/ß 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.,,pubmed:38570687,,PHBC endothelial cells 30 hpf WT 4,GSM7429325,,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 “—outFilterMismatchNoverLmax 0.1” 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,,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 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® 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.,,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 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® 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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP439616,,loader:fastq load.py,B4_WT_R1.fastq.gz B4_WT_R2.fastq.gz,fastq fastq,2924689332.0,19639070.0,GSM7429325 r1,,A:809211667;C:649768099;G:647294872;T:816789532;N:1625162,,,,,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,,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/ß catenin signaling in CNS angiogenesis we compared the bulk transcriptomes of WT and Wnt/ß catenin signaling deficient PHBC endothelial cells prior to CNS vascular invasion. To this end we used three approaches to abrogate endothelial Wnt/ß 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/ß 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.,,pubmed:38570687,,PHBC endothelial cells 30 hpf WT 3,GSM7429324,,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 “—outFilterMismatchNoverLmax 0.1” 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,,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 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® 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.,,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 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® 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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP439616,,loader:fastq load.py,B3_WT_R1.fastq.gz B3_WT_R2.fastq.gz,fastq fastq,2556876101.0,17158306.0,GSM7429324 r1,,A:674099968;C:605785858;G:602757969;T:672809126;N:1423180,,,,,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,,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/ß catenin signaling in CNS angiogenesis we compared the bulk transcriptomes of WT and Wnt/ß catenin signaling deficient PHBC endothelial cells prior to CNS vascular invasion. To this end we used three approaches to abrogate endothelial Wnt/ß 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/ß 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.,,pubmed:38570687,,PHBC endothelial cells 30 hpf WT 2,GSM7429323,,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 “—outFilterMismatchNoverLmax 0.1” 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,,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 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® 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.,,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 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® 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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP439616,,loader:fastq load.py,B2_WT_R1.fastq.gz B2_WT_R2.fastq.gz,fastq fastq,2719619180.0,18253304.0,GSM7429323 r1,,A:737514407;C:623462360;G:618552838;T:738582283;N:1507292,,,,,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,,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/ß catenin signaling in CNS angiogenesis we compared the bulk transcriptomes of WT and Wnt/ß catenin signaling deficient PHBC endothelial cells prior to CNS vascular invasion. To this end we used three approaches to abrogate endothelial Wnt/ß 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/ß 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.,,pubmed:38570687,,PHBC endothelial cells 30 hpf WT 1,GSM7429322,,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 “—outFilterMismatchNoverLmax 0.1” 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,,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 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® 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.,,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 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® 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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP439616,,loader:fastq load.py,B1_WT_R1.fastq.gz B1_WT_R2.fastq.gz,fastq fastq,3264716585.0,21921700.0,GSM7429322 r1,,A:879625441;C:754137197;G:748183608;T:880983333;N:1787006,,,,,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,,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/ß catenin signaling in CNS angiogenesis we compared the bulk transcriptomes of WT and Wnt/ß catenin signaling deficient PHBC endothelial cells prior to CNS vascular invasion. To this end we used three approaches to abrogate endothelial Wnt/ß 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/ß 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.,,pubmed:38570687,,Endothelial cells 30 hpf negative 3,GSM7429321,,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 “—outFilterMismatchNoverLmax 0.1” 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,,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 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® 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.,,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 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® 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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP439616,,loader:fastq load.py,A3_Neg_controls_R1.fastq.gz A3_Neg_controls_R2.fastq.gz,fastq fastq,2754470229.0,18487768.0,GSM7429321 r1,,A:707439749;C:673922384;G:669885592;T:701717257;N:1505247,,,,,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,,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/ß catenin signaling in CNS angiogenesis we compared the bulk transcriptomes of WT and Wnt/ß catenin signaling deficient PHBC endothelial cells prior to CNS vascular invasion. To this end we used three approaches to abrogate endothelial Wnt/ß 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/ß 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.,,pubmed:38570687,,Endothelial cells 30 hpf negative 2,GSM7429320,,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 “—outFilterMismatchNoverLmax 0.1” 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,,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 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® 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.,,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 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® 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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP439616,,loader:fastq load.py,A2_Neg_controls_R1.fastq.gz A2_Neg_controls_R2.fastq.gz,fastq fastq,2820835655.0,18927799.0,GSM7429320 r1,,A:731665823;C:680271247;G:678251388;T:729095004;N:1552193,,,,,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,,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/ß catenin signaling in CNS angiogenesis we compared the bulk transcriptomes of WT and Wnt/ß catenin signaling deficient PHBC endothelial cells prior to CNS vascular invasion. To this end we used three approaches to abrogate endothelial Wnt/ß 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/ß 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.,,pubmed:38570687,,Endothelial cells 30 hpf negative 1,GSM7429319,,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 “—outFilterMismatchNoverLmax 0.1” 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,,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 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® 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.,,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 250–500 pg total RNA was used as input for SMART Seq® v4 Ultra® 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.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP439616,,loader:fastq load.py,A1_Neg_controls_R1.fastq.gz A1_Neg_controls_R2.fastq.gz,fastq fastq,3578902225.0,24014303.0,GSM7429319 r1,,A:937280207;C:855762487;G:851738460;T:932155139;N:1965932,,,,,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,,Germany,2023-05-25,Pharyngula,Embryo,Endothelium,Cardiovascular System