run_metadata: 71811

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
71811	SRR22058440	SRX18039491	SRS15546048	SRP404726	PRJNA894687	hapln1a+ cells guide coronary growth during heart morphogenesis and regeneration [Dev tcf21+ cells]	GSE216648	Other	As cardiac regeneration requires new coronary vessels exploring the underlying mechanisms behind revascularization will facilitate the development of regenerative therapies for heart failure. Although multiple tissues and chemokines likely orchestrate coronary formation the interaction between coronary growth and guidance cues remains unclear. Here by applying single cell RNA sequencing scRNA seq analysis we examined gene expression in zebrafish epicardial cells during coronary vascularization and identified hapln1a expressing epicardial cells enriched with vascular regulating genes. Fluorescence reporter assays indicated hapln1a+ cells not only envelop coronary vessels but also form cellular shear structures in ahead of coronary tips. Live imaging analyses demonstrated coronary growth along the pre formed shears with depletion of hapln1a+ cells blocking this growth. Further we found hapln1a+ cells also pre lead coronary tips in the regenerating area and hapln1a+ cell loss inhibits coronary revascularization. To characterize the molecular nature of hapln1a+ cells during coronary growth we profiled hapln1a+ cells in juvenile and regenerating hearts and detected expression of the cell adhesion and migration regulator serpine1 in hapln1a+ cells adjacent to coronary tips. Pharmacological inhibition of serpine1 function blocked coronary vascularization and revascularization. Altogether our studies reveal that hapln1a+ cells are required for coronary production during heart morphogenesis and regeneration by establishing a microenvironment to facilitate guided coronary growth. Overall design: Epicardial cells of zebrafish heart were isolated by Fluorescence activated cell sorting FACS according to the presence or absence of eGFP signal and analyzed using scRNAseq.	parent bioproject:PRJNA894685	pubmed:37311876		tcf21+ development scRNAseq	GSM6685266		source name:heart\|strain:EK\|tissue:heart\|cell type:epicardial cells\|age:7 weeks\|geo loc name:missing\|collection date:missing	tcf21+ development scRNAseq	All processing was performed in 10X Genomics CellRanger v3.1.0 using default parameters Assembly: Danio rerio GRCz11 Supplementary files format and content: Cell Ranger outputs a .mtx file with the feature barcode matrix. This matrix contains the counts of molecules per cell UMI/cell as determined post filtering and counting by Cell Ranger. The matrix is in market exchange format while the row gene or feature and columns cell barcodes are provided as TSV files. File formats are documented in the Cell Ranger software manual	heart		Hearts were dissected from juvenile zebrafish and ventricles were digested with Liberase TM 0.26 U/ml . Dissociated cells were spun down and live EGFP+ cells were sorted by flow cytometry. Library was performed according to the manufacter’s instructions single cell 3’ v3.1 protocol 10x Genomics		strain:EK\|tissue:heart\|cell type:epicardial cells\|cell type sorted:tcf21+\|age:7 weeks	GSM6685266	GSM6685266: tcf21+ development scRNAseq; Danio rerio; RNA Seq	GSM6685266 r1	GSM6685266	1	Hearts were dissected from juvenile zebrafish and ventricles were digested with Liberase TM 0.26 U/ml . Dissociated cells were spun down and live EGFP+ cells were sorted by flow cytometry. Library was performed according to the manufacter's instructions single cell three prime v3.1 protocol 10x Genomics		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 550		SRP404726			TCF_21_S1_L001_R1_001.fastq.gz TCF_21_S1_L001_R2_001.fastq.gz	fastq fastq	19362384447.0	162709113.0	GSM6685266 r1	0:28 1:91	A:5391284818;C:4382019183;G:4643235756;T:4943804153;N:2040537	28	91			5391284818	4382019183	4643235756	4943804153	2040537	SRX18039491	SRS15546048	SRA1528514	Emory University	Emory University	2	0.00432	0.90419	0.00171	0.10489	0.9947	0.84737	0.31827	0.50898	28	91	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x		United States	2022-10-26	Juvenile	Juvenile	Heart	Cardiovascular System