{"database": "metadata", "table": "run_metadata", "rows": [[58577, "SRR11420468", "SRX7998904", "SRS6376267", "SRP254020", "PRJNA615175", "A Zebrafish Based Orthotopic Glioblastoma Xenograft Model for Preclinical Drug Screening and Clinical Drug Sensitivity Prediction", "GSE147526", "Other", "A reliable animal model that can mimic the GBM intracranial infiltration and Blood brain barrier BBB interaction is necessary for effective therapeutics development. Here  we report a zebrafish based orthotopic GBM xenograft model  in which GBM cells from different species and even patients  can robustly propagate and faithfully reproduce their histological characteristics. Single cell RNA seq indicates a transcriptomic adaption of GBM xenografts to infiltrative phenotype within the zebrafish brains. We also provide evidence that the BBB in zebrafish larva is molecularly and functionally intact and can interact with GBM cells in similar ways as in mammals  which together enables this model to accurately identify BBB penetrating drugs. Using GBM patients' samples  we further generate zebrafish patient derived orthotopic xenografts z PDOX and proof of concept experiments indicate the short term temozolomide response in z PDOX can predict the long term prognosis of corresponding GBM patients. These together illustrate the value of zebrafish GBM model in drug discovery and precision medicine. Overall design: 1.Single cell RNA seq for endothelial cells of zebrafish 2.Single cell RNA seq for GBM cells implanted in zebrafish brain", null, "pubmed:35199829", null, "Smartseq2 AXL A2 endo Danio", "GSM4432615", null, "tissue:endothelial cells|strain:flk:GFP|cell tye:endothelial cells", "Smartseq2 AXL A2 endo Danio", "ScRNA seq alignment process was completed by STAR 2.6.0a DESeq2 standard workflow Genome build: GRCz10 genome references for Zebrafish and GRCh38 genome references for human Supplementary files format and content: csv files with raw counts and FPKM", "endothelial cells", null, "1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope  the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope  a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle.   2. For GBM cells  zebrafish were injected with GBM U251 mCherry cells  and allowed to form widespread  tumor invasion for xxx 5 days. At that point  the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope  the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously  GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the 3\u2019 scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang  2010.", null, "strain:flk:GFP|cell tye:endothelial cells", "GSM4432615", "GSM4432615: Smartseq2 AXL A2 endo Danio; Danio rerio; RNA Seq", "GSM4432615", null, "1", "1. The flk:GFP zebrafish were used to obtain endothelial cells. Under the stereomicroscope  the brains of the zebrafish larvae were isolated using tweezers. The brain and body of zebrafish were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Under the fluorescence stereomicroscope  a single GFP expressing endothelial cell from cell suspension was sucked up by a borosilicate glass needle.   2. For GBM cells  zebrafish were injected with GBM U251 mCherry cells  and allowed to form widespread  tumor invasion for xxx 5 days. At that point  the brains of the zebrafish larvae were isolated using tweezers. Under the fluorescence stereomicroscope  the core area and tumor invasion area of the glioma xenografts from the zebrafish brain were divided into two dishes  and completely disaggregated using 1mg/ml papain and 1mg/ml DNase at 37\u00b0C for 30min. post digestion  a single cell suspension was made by resuspending the cells in DMEM with 2% FBS. Simultaneously  GBM U251 mCherry cells maintained in culture were trypsinized and resuspended in DMEM with 2% FBS. Single cells from cell suspension was sucked up into a vial containing lysis buffer by a borosilicate glass needle. Follwed by v2 protocol of chemistry of the three prime scRNA seq 10X genomics platform and modified SMART seq2 protocol based on published previously Fuchou Tang  2010.", "GEO Accession:GSM4432615", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP254020", null, null, "AXL-A2_HHVK7CCXY_L3_1.clean.fq.gz AXL-A2_HHVK7CCXY_L3_2.clean.fq.gz", "fastq fastq", 1474053600.0, 4913512.0, "GSM4432615 r1", "0:150 1:150", "A:409235463;C:294510014;G:304366926;T:465858337;N:82860", 150, 150, null, null, 409235463, 294510014, 304366926, 465858337, 82860, "SRX7998904", "SRS6376267", "SRA1059261", "GEO", "Chen & Liu Lab, State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University., Sichuan University", 2, 0.89481, 0.90098, 0.57187, 0.57596, 0.91045, 0.91366, 0.46573, 0.46566, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "China", "2020-03-25", "Larval", "Larval", "Endothelium", "Cardiovascular System"]], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": ["rowid"], "primary_key_values": ["58577"], "units": {}, "query_ms": 13.031718001002446}