run_metadata: 55797

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
55797	SRR10753172	SRX7427898	SRS5873831	SRP238479	PRJNA597148	Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle	GSE142484	Transcriptome Analysis	During vertebrate embryogenesis vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each		pubmed:32493965		Jul11 2016 15 18ss etv2gfp	GSM4230286		tissue:Vascular Endothelial Cells\|cell type:Vascular Endothelial Cells\|animal line:Tg 2.3 etv2:GFPzf372\|developmental stage:15 18 somite stage	Jul11 2016 15 18ss etv2gfp	Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72	Vascular Endothelial Cells	No treatment	Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells	Embryos grown in standard E3 medium at 28.5C	cell type:Vascular Endothelial Cells\|animal line:Tg 2.3 etv2:GFPzf372\|developmental stage:15 18 somite stage	GSM4230286	GSM4230286: Jul11 2016 15 18ss etv2gfp; Danio rerio; RNA Seq	GSM4230286		1	Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells	GEO Accession:GSM4230286	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP238479			run1696_lane2_read1_indexN704-S503=Jul11_Cell_11.fastq.gz run1696_lane2_read2_indexN704-S503=Jul11_Cell_11.fastq.gz	fastq fastq	263149800.0	1754332.0	GSM4230286 r11	0:75 1:75	A:73836706;C:57360247;G:57722644;T:74193453;N:36750	75	75			73836706	57360247	57722644	74193453	36750	SRX7427898	SRS5873831	SRA1015481	GEO	Developmental Biology, Cincinnati Children's Hospital Medical Center	2	0.89945	0.90639	0.23998	0.24336	0.91133	0.91086	0.51231	0.51605	75	75	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown		United States	2019-12-21	Segmentation	Embryo	Endothelium	Cardiovascular System