run_metadata: 49615

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
49615	SRR7989637	SRX4820827	SRS3895219	SRP164769	PRJNA495391	Wnt/ß catenin signaling regulates VE cadherin mediated anastomosis of brain capillaries by counteracting S1pr1 signaling	GSE121041	Transcriptome Analysis	Canonical Wnt signaling is crucial for vascularization of the central nervous system and blood brain barrier BBB formation. BBB formation and modulation are not only important for development but also relevant for vascular and neurodegenerative diseases. However beyond the early requirement of Wnt signaling for brain capillary development there is little understanding of how Wnt signaling further contributes to brain angiogenesis and BBB formation. By combining high resolution in vivo imaging with temporally and spatially controlled manipulation of Wnt signaling we were able to dissect different requirements for Wnt signaling during brain angiogenesis and BBB formation. In the absence of Wnt signaling premature Sphingosine 1 phosphate receptor S1pr signaling leads to a reduction of VE cadherin and Esama at cell cell junctions. Wnt signaling most likely suppresses S1pr signaling during angiogenesis to enable the dynamic junction formation during anastomosis whereas later S1pr signaling regulates BBB maturation and VE cadherin stabilization. Our data provides a novel link between brain capillary angiogenesis and BBB formation and identifies Wnt signaling as coordinator of the timing and as regulator of anastomosis. Overall design: Isolation of the zebrafish CtA endothelial cells from 36hpf old Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos treated with IWR 1 or DMSO		pubmed:30451830;pubmed:38570687		DMSO rep2	GSM3424987		source name:brain endothelial cells\|lines:Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos\|tissue:hindbrain endothelium\|age:36hpf	DMSO rep2	Raw reads were assessed for quality adapter content and duplication rates with FastQC available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reaper version 13 100 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides82. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 GRCz10.87 using STAR 2.4.0a with the parameter “ outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.4.5 p1 tool from the Subread package84. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Genome build: DanRer10 Supplementary files format and content: tab delimited text files include library size normlized counts per gene	brain endothelial cells		Photoconversion of Kaede fluorescent protein was performed by scanning the selected region of interest with a 405 nm diode laser 100% laser 5 iterations 50s. post several washes in HBSS Hank’s Balanced Salt Solution Gibco without xxx+/Mg2+ zebrafish embryos dissociation was performed at 28.5 °C during 30 min using 2 mL of trypsin LE select Gibco. Photoswitched ECs were isolated on FACS Aria II. Cells were immediately centrifuged frozen by liquid nitrogen and stored at 80°C. RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen 250 500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.		lines:Tgfli1a:Gal4ubs3;UAS:Kaederk8 embryos\|tissue:hindbrain endothelium\|age:36hpf	GSM3424987	GSM3424987: DMSO rep2; Danio rerio; RNA Seq	GSM3424987		1	Photoconversion of Kaede fluorescent protein was performed by scanning the selected region of interest with a 405 nm diode laser 100% laser 5 iterations 50s. post several washes in HBSS Hank's Balanced Salt Solution Gibco without xxx+/Mg2+ zebrafish embryos dissociation was performed at 28.5 °C during 30 min using 2 mL of trypsin LE select Gibco. Photoswitched ECs were isolated on FACS Aria II. Cells were immediately centrifuged frozen by liquid nitrogen and stored at 80°C. RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen 250 500 pg total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.	GEO Accession:GSM3424987	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP164769			vanHollebeke_WT_2_R1.fastq.gz	fastq	2807935583.0	38002656.0	GSM3424987 r1	0:73.89 1:0	A:815631502;C:589381721;G:586257915;T:816652021;N:12424	73	0			815631502	589381721	586257915	816652021	12424	SRX4820827	SRS3895219	SRA791232	GEO	MPI for heart and lung research	1	0.84347		0.20267		0.77419		0.51656		75		B		usable mapping rate	illumina	nextseq	full_length	cdna_unspecified	unknown	sc	single_cell_plate	smartseq		Germany	2018-10-09	Pharyngula	Embryo	Multi-tissue	Multi-system