run_metadata: 58568

This data as json

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
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