{"database": "metadata", "table": "run_metadata", "rows": [[32806, "SRR29478752", "SRX24989905", "SRS21691708", "SRP515053", "PRJNA1126173", "Endolysosomal dysfunction in radial glia progenitor cells leads to defective cerebral angiogenesis and compromised blood brain barrier integrity", "GSE270309", "Transcriptome Analysis", "The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity.  While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration  the underlying molecular mechanisms remain unclear.  Here  we use zebrafish embryos carrying a mutation in Scavenger Receptor B2  a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs  to investigate the interplay among different NVU components. Through live imaging and genetic manipulations  we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling  thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling  leading to severe vascular defects  hemorrhages  and a leaky BBB. Altogether  our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity.  While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration  the underlying molecular mechanisms remain unclear.  Here  we use zebrafish embryos carrying a mutation in Scavenger Receptor B2  a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs  to investigate the interplay among different NVU components. Through live imaging and genetic manipulations  we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling  thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling  leading to severe vascular defects  hemorrhages  and a leaky BBB. Altogether  our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. The neurovascular unit NVU is a complex multicellular structure that helps maintain cerebral homeostasis and blood brain barrier BBB integrity.  While extensive evidence links NVU alterations to cerebrovascular diseases and neurodegeneration  the underlying molecular mechanisms remain unclear.  Here  we use zebrafish embryos carrying a mutation in Scavenger Receptor B2  a highly conserved endolysosomal protein expressed predominantly in Radial Glia Cells RGCs  to investigate the interplay among different NVU components. Through live imaging and genetic manipulations  we demonstrate that compromised acidification of the endolysosomal compartment in mutant RGCs leads to impaired Notch3 signaling  thereby inducing excessive neurogenesis and reduced glial differentiation. We further demonstrate that alterations to the neuron/glia balance result in impaired VEGF and Wnt signaling  leading to severe vascular defects  hemorrhages  and a leaky BBB. Altogether  our findings provide novel insights into NVU formation and function and offer new avenues for investigating diseases involving white matter defects and vascular abnormalities. Overall design: 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension . Sorting and RNA extraction was performed on TgBACscar2ba:KalTA4; UAS mKate2", null, "pubmed:39289367", null, "head  scarb2a mut  rep 3", "GSM8339369", null, "source name:head|tissue:head|cell type:scarb2a+ cells|genotype:scarb2a mut|geo loc name:missing|collection date:missing", "head  scarb2a mut  rep 3", "done using the User friendly Transcriptomic Analysis Pipeline Assembly: danRer11 Supplementary files format and content: countsMatrix normalized.txt: expression dataset   txt file contaning normalized UMI counts table for all samples.", "head", null, "For each experimental condition  a pool of 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension. post a brief enzymatic treatment with a cocktail of Liberase Blendzyme 3 Roche  trypsin B BI  and DNAseI Roche  the cell suspension was strained through a 70\u00b5m filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 \u00b5l of lysis/binding buffer solution ThermoFisher containing RNase inhibitor RNasinTM Promega. FACS analysis and sorting were performed on a BD FACS Aria III using a 70\u00b5m nozzle. RNA was captured using Dynabeads\u2122 mRNA DIRECT\u2122 Purification Kit ThermoFisher prior to library preparation. A bulk adaptation of the MARS seq protocol was used to generate RNA libraries for the expression profile of scarb2+ mutant and wt cells. The RNA was further fragmented and transformed into a sequencing ready library by tagging the samples with Illumina sequences during ligation  RT  and PCR.  The final library concentration was measured by Qubit  TapeStation  and qPCR for zebrafish actin as previously described. Sequencing was performed on a Nextseq500/550 High Output Kit v2.5 75 cycles Illumina; paired end sequencing  and each sample was sequenced for 6M reads.", null, "tissue:head|cell type:scarb2a+ cells|genotype:scarb2a mut", "GSM8339369", "GSM8339369: head  scarb2a mut  rep 3; Danio rerio; RNA Seq", "GSM8339369 r1", "GSM8339369", "1", "For each experimental condition  a pool of 50 heads 3 biological replicates was dissected from euthanized 48 hpf scarb2a mutants and wt siblings and dissociated into a single cell suspension. post a brief enzymatic treatment with a cocktail of Liberase Blendzyme 3 Roche  trypsin B BI  and DNAseI Roche  the cell suspension was strained through a 70\u00b5m filter and stained with SYTOXTM blue ThermoFisher for live/dead discrimination. 5000 live scarb2a+ single cells were sorted into 40 \u00b5l of lysis/binding buffer solution ThermoFisher containing RNase inhibitor RNasinTM Promega. FACS analysis and sorting were performed on a BD FACS Aria III using a 70\u00b5m nozzle. RNA was captured using Dynabeads\u2122 mRNA DIRECT\u2122 Purification Kit ThermoFisher prior to library preparation. A bulk adaptation of the MARS seq protocol was used to generate RNA libraries for the expression profile of scarb2+ mutant and wt cells. The RNA was further fragmented and transformed into a sequencing ready library by tagging the samples with Illumina sequences during ligation  RT  and PCR.  The final library concentration was measured by Qubit  TapeStation  and qPCR for zebrafish actin as previously described. Sequencing was performed on a Nextseq500/550 High Output Kit v2.5 75 cycles Illumina; paired end sequencing  and each sample was sequenced for 6M reads.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP515053", null, null, "scarb2_mut3_R2.fastq.gz scarb2_mut3_R1.fastq.gz", "fastq fastq", 590803877.0, 7118119.0, "GSM8339369 r1", "0:75 1:8", "A:171152826;C:118382558;G:138973475;T:162287717;N:7301", 75, 8, null, null, 171152826, 118382558, 138973475, 162287717, 7301, "SRX24989905", "SRS21691708", "SRA1904886", "Karina Yaniv lab, Immunology and Regenerative Biology, Weizmann Institute of Science", "Karina Yaniv lab, Immunology and Regenerative Biology, Weizmann Institute of Science", 2, 0.86187, 0.0, 0.06751, 0.0, 0.80081, 1.0, 0.47421, null, 75, 8, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "marsseq", null, "Israel", "2024-06-20", "Hatching", "Embryo", "Head", "Nervous 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": ["32806"], "units": {}, "query_ms": 9.695218002889305}