{"database": "metadata", "table": "run_metadata", "rows": [[75674, "SRR24758234", "SRX20534082", "SRS17842609", "SRP440051", "PRJNA977246", "An organ specific angiogenic control mechanism for endothelial tailoring", "GSE233662", "Transcriptome Analysis", "Each organ of the human body requires locally adapted blood vessels. The gain of such organotypic vessel specializations is often deemed molecularly unrelated to the process of organ vascularization. Opposing this model  we reveal a molecular mechanism for brain specific angiogenesis  that operates under the control of Wnt7a/b ligands  well known blood brain barrier maturation signals. The control mechanism relies on Wnt7a/b dependent expression of Mmp25 in brain endothelial cells. This hitherto poorly characterized GPI anchored matrix metalloproteinase is selectively required in endothelial tip cells to enable their initial migration across the pial basement membrane lining the brain surface  which distinctive molecular composition is controlled by embryonic pial fibroblasts. Mechanistically  Mmp25 confers brain invasive competence by cleaving the pial basement membrane enriched Col4a5/6 within a short non collagenous region of the central helical part of the heterotrimer. Upon genetic interference with pial basement membrane composition  the Wnt/\u00df catenin dependent organotypic control of brain angiogenesis is lost  resulting in properly patterned  yet blood brain barrier defective cerebrovasculatures. This work reveals an organ specific angiogenesis mechanism  sheds light on tip cell mechanistic angiodiversity  and thereby illustrates how organs  by imposing local constraints on angiogenic tip cells  can select vessels matching their distinctive physiological requirements. Overall design: The samples in this submission are single cells  sorted into single wells of a 96 or 384 well plates. The cells were lysed and transcriptomic sequencing data was obtained using Smart seq2 chemistry", null, "pubmed:38570687", null, "Photoconverted brain endothelial cells  rep2", "GSM7432137", null, "source name:Brain|tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino|geo loc name:missing|collection date:missing", "Photoconverted brain endothelial cells  rep2", "Demultiplexing with bcl2fastq Alignment against the zebrafish Danio rerio.GRCz11.95 build using Bowtie2 Removal of adapter sequencing with TrimGalore Removal of duplets using samtools Generation of a count matrix with FeatureCounts from the SubRead package Assembly: Danio.Rerio.GRCz11 Supplementary files format and content: Count files  with every column a cell and every row a gene.", "Brain", "Morpholino injection", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank\u2019s Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", "Standard", "tissue:Brain|age:30 hpf|cell type:Endothelial cells|genotype:Tgfli1a:Gal4FF;UAS:Kaede|treatment:WT and gpr124 morpholino", "GSM7432137", "GSM7432137: Photoconverted brain endothelial cells  rep2; Danio rerio; RNA Seq", "GSM7432137 r1", "GSM7432137", "1", "Photoconversion ofTgfli1:Gal4ubs3;UAS:Kaederk8PHBC or CtAs ECs was performed using a Zeiss LSM 710 confocal microscope Carl Zeiss  objective lenses: Plan Apochromat \u00d720/0.8 M27. Briefly  anesthetised embryos were mounted laterally in 1% low melting agarose and the fluorescent Kaede protein was photoswitched by scanning the selected region of interest with a 405\u2009nm laser five iterations of 50\u2009s. post isolation from the agarose  embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution  Gibco and dissociated at 28.5\u2009\u00b0C for 30\u2009min in TrypLE select Thermo Fischer Scientific  12563011. Dissociation was stopped by the addition of FBS and centrifugation. The cell pellet was resuspended in HBSS containing Ca2+/Mg2+and 5% FBS  filtered  and submitted to FACS BD Biosciences FACSAria III. Single cell cDNA libraries were prepared according to the established protocol for Smart Seq2. In brief  poly adenylated mRNA was transcribed to cDNA using oligodT primer and SuperScript II reverse transcriptase ThermoFisher Scientific. Synthesis of second strand cDNA was achieved using a template switching oligo  and the double stranded cDNA was then amplified using polymerase chain reaction PCR for 23 \u2013 26 cycles. post bead purification  overall cDNA quality was controlled QC by analyzing randomly selected single cell samples wells on a 2100 Bioanalyzer with a DNA High sensitivity chip Agilent Biotechnologies. When the sample plate passed the QC  the cDNA was fragmented and tagged tagmented using Tn5 transposase  and each single cell sample well was uniquely indexed using Illumina Nextera XT index kits set A D. Therepost  the indexed single cell samples from one plate were pooled to be sequenced together on one lane of a HiSeq3000/4000 sequencer Illumina  using dual indexing and 50 base read length. ScRNA Seq with Smart seq2", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP440051", null, "loader:fastq load.py", "GC049751_A03.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz", "fastq", 182987337.0, 3587987.0, "GSM7432137 r3", "0:51", "A:48471316;C:41287723;G:41835653;T:51376450;N:16195", 51, null, null, null, 48471316, 41287723, 41835653, 51376450, 16195, "SRX20534082", "SRS17842609", "SRA1645745", "SICOF, Department of Medicine, Huddinge, Karolinska Institute", "Department of Medicine, Karolinska Institute", 1, 0.79625, null, 0.12945, null, 0.87042, null, 0.54466, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "poly_a", "nextera", "sc", "single_cell_plate", "smartseq", null, "Sweden", "2023-05-29", "Pharyngula", "Embryo", "Brain", "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": ["75674"], "units": {}, "query_ms": 16.161571998964064}