run_metadata: 75734

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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
75734	SRR24758294	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/ß 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		pubmed:38570687		Photoconverted brain endothelial cells rep2	GSM7432137		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 ×20/0.8 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 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank’s Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min 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 – 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 ×20/0.8 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 nm laser five iterations of 50 s. post isolation from the agarose embryos were washed in Ca2+/Mg2+ free HBSS Hank's Balanced Salt Solution Gibco and dissociated at 28.5 °C for 30 min 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 – 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		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 4000		SRP440051		loader:fastq load.py	GC049751_G12.180302.HiSeq4000.FCA.lane5.gcap_17_11.R1.fastq.gz	fastq	326298.0	6398.0	GSM7432137 r84	0:51	A:79720;C:78815;G:72411;T:95325;N:27	51				79720	78815	72411	95325	27	SRX20534082	SRS17842609	SRA1645745	SICOF, Department of Medicine, Huddinge, Karolinska Institute	Department of Medicine, Karolinska Institute	1	0.62417		0.09728		0.9694		0.56033		51		B		usable mapping rate	illumina	hiseq_era	unknown	poly_a	nextera	sc	single_cell_plate	smartseq		Sweden	2023-05-29	Pharyngula	Embryo	Brain	Nervous System