run_metadata: 68657

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
68657	SRR18097958	SRX14248906	SRS12068874	SRP360907	PRJNA809307	Generation of specialized blood vessels via lymphatic transdifferentiation	GSE197161	Transcriptome Analysis	The lineage and developmental trajectory of a cell are key determinant s of cellular identity. In the vascular system endothelial cells ECs of blood and lymphatic vessels LVs differentiate and diversify to cater the different physiological demands of each organ . While LVs are known to originate from multiple origins lymphatic ECs LECs themselves are not known to generate other cell types . Here we u s e recurrent imaging and lineage tracing of ECs in zebrafish anal fins AF from early development through maturity to uncover an unexpected mechanism of specialized blood vessel formation through transdifferentiation of LECs . Moreover we demonstrate distinct functional implications for deriving AF vessels from either LECs or blood ECs uncovering a link between cell ontogeny and functionality. We further use scRNA seq to characterize the different cellular populations and transition states involved in the transdifferentiation process . Finally we show that akin to its normal development the vasculature is re derived from lymphatics during AF regeneration demonstr ating that LECs in adult fish retain both potency and plasticity for generating blood ECs . Overall our work highlights a new innate mechanism of blood vess el formation through LEC trans differentiation and provides in vivo evidence for a link between cell ontogeny and functionality in ECs Overall design: 80 anal fins from immature zebrafish were digested. Sorting and RNA extraction was performed on fli1a:dsRed positive cells		pubmed:35614218		Immature fin ECs plate2	GSM5910459		source name:fli1a:dsRed positive cells\|tissue:Anal fin\|cell type:endothelial cells\|Stage:II III	Immature fin ECs plate2	GRCz10 genome mapping was done using Bowtie2 with default parameters Demultiplexing and UMI count matrixes were based on 4bp pool barcodes in Read1 for each sample. 8bp of UMI with 7bp of cell barcodes in Read2 and performed as described in Jaitin et al. 2014 Genome build: GRCz10 Supplementary files format and content: AB006.txt AB007.txt AB008.txt: expression dataset txt files containing UMI counts table per plate. Single cell metadata p1.xslx: xslx file sheet1 pool barcode of plate1 sheet2 cell barcodes and coordinates required for MARS seq pipeline Jaitin et al. 2014 sheet3 plate1 analyzed cell names. Single cell metadata p2.xslx: xslx file sheet1 pool barcode of plate2 sheet2 cell barcodes and coordinates required for MARS seq pipeline Jaitin et al. 2014 sheet3 plate2 analyzed cell names. Single cell metadata p3.xslx: xslx file sheet1 pool barcode of plate3 sheet2 cell barcodes and coordinates required for MARS seq pipeline Jaitin et al. 2014 sheet3 plate3 analyzed cell names	fli1a:dsRed positive cells		80 anal fins were dissected manually chopped with a sterile razor and enzymatically digested using Liberase I Trypsin B and DNaseI. Single cells were sorted into 384 well plates containing lysis solution UPW 8nM poly dT barcodes 0.1%triton and RNAse inhibitor MARS seq libraries were prepared as described Jaitin et al Science 2014		tissue:Anal fin\|cell type:endothelial cells\|Stage:II III	GSM5910459	GSM5910459: Immature fin ECs plate2; Danio rerio; RNA Seq	GSM5910459 r1	GSM5910459	1	80 anal fins were dissected manually chopped with a sterile razor and enzymatically digested using Liberase I Trypsin B and DNaseI. Single cells were sorted into 384 well plates containing lysis solution UPW 8nM poly dT barcodes 0.1%triton and RNAse inhibitor MARS seq libraries were prepared as described Jaitin et al Science 2014		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP360907			BC2_S0_R1_001.fastq.gz BC2_S0_R2_001.fastq.gz	fastq fastq	4158365400.0	46204060.0	GSM5910459 r1	0:75 1:15	A:1056133752;C:954371027;G:1117373354;T:1029764959;N:722308	75	15			1056133752	954371027	1117373354	1029764959	722308	SRX14248906	SRS12068874	SRA1376737	Weizmann Institute of Science	Department of Biological Regulation, Weizmann Institute of Science	2	0.76282	0.0	0.2382	0.0	0.87158	1.0	0.53888		75	15	B	T	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_plate	marsseq		Israel	2022-02-22	Undetermined	Adult	Fin	Surface Structure