run_metadata: 72819

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
72819	SRR23190058	SRX19140398	SRS16550346	SRP418629	PRJNA926357	Single cell transcriptional profiles of endothelial cells sorted from the hearts with ablation of Wnt/beta catenin signaling activating cardiomyocytes and without xxx [scRNA seq]	GSE223461	Transcriptome Analysis	To understand how Wnt/ß catenin signaling activated cardiomyocytes ß cat ON CMs promote coronary vessel development we performed single cell RNA sequencing of endothelial cells ECs sorted from the hearts ablated ß cat ON CMs and those from control hearts respectively. Our analyses indicated that ß cat ON CMs regulates coronary vessel development by promoting arterialization a step in the transition of endocardial ECs to coronary ECs. Overall design: To induce nitroreductase metronidazole NTR MTZ dependent ablation of ß cat ON CMs we treated 5 mM MTZ or DMSO to Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCF?C;5xUAS:NTR mCherry fish every other day for 4 weeks from 1 mpf. We isolated live GFP+ cells by FACS sorting from the fish treated MTZ or DMSO respectively. Barcoded single cell cDNA libraries were prepared using the Chromium Next GEM single cell three primereagent kits v3.1 and sequenced using Illumina NextSeq 500.	parent bioproject:PRJNA926354	pubmed:39395410		EC MTZ scRNAseq	GSM6956592		source name:Heart\|tissue:Heart\|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry\|cell type:Endothelial cells\|treatment:MTZ	EC MTZ scRNAseq	The 10x Genomics Cell Ranger pipeline v6.1.1 was used to perform sample demultiplexing alignment to the reference genome Danio rerio GRCz11 barcode/UMI processing and gene counting for each cell. Assembly: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample mtx files count gene UMI couns for each sample	Heart	Fish were treated with DMSO or 5 mM MTZ dissolved in fish water for 12 h in the dark. post exposure to chemicals the water was changed to remove the chemicals and the fish were kept in the tank without xxx circulation. Chemicals were treated every other day.	Hearts were resected from Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated DMSO or 5 mM MTZ for 4 weeks from 1 mpf. The resected hearts were collected into a 35 mm dish containing HBSS without xxx and magnesium. Hearts were torn and were transferred into a 12 well plate. The hearts were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected into low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain Thermofisher Scientific S34857 and sorted by a FACSFusion cell sorter BD Bioscience. Sorted cells were collected in 1% FBS/DMEM and counted by a cell counter Thermofisher scientific. The resulting endothelial cellular suspension was loaded on a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell 3’reagent kits v3.1 10X Genomics 1000128 according to the manufacturer’s protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.		tissue:Heart\|genotype:Tgfli1:EGFP;Tgcryaa:EGFP myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry\|cell type:Endothelial cells\|treatment:MTZ	GSM6956592	GSM6956592: EC MTZ scRNAseq; Danio rerio; RNA Seq	GSM6956592 r1	GSM6956592	1	Hearts were resected from Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated DMSO or 5 mM MTZ for 4 weeks from 1 mpf. The resected hearts were collected into a 35 mm dish containing HBSS without xxx and magnesium. Hearts were torn and were transferred into a 12 well plate. The hearts were digested with 3 mg/ml collagenase type IV Worthington LS004188/HBSS for 30 min at 28.5 ºC. post pipetting the cells were collected into low binding tubes pelleted 3000 rpm 5 min at 4ºC and washed in 0.5% FBS/DMEM phenol red free. The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain Thermofisher Scientific S34857 and sorted by a FACSFusion cell sorter BD Bioscience. Sorted cells were collected in 1% FBS/DMEM and counted by a cell counter Thermofisher scientific. The resulting endothelial cellular suspension was loaded on a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell three primereagent kits v3.1 10X Genomics 1000128 according to the manufacturer's protocol. Following droplet generation and barcoding cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	NextSeq 500		SRP418629		loader:fastq load.py\|options: readTypes=BBTT read1PairFiles=M S1 L001 R1 001.fastq.gz read2PairFiles=M S1 L001 R2 001.fastq.gz read3PairFiles=M S1 L001 I1 001.fastq.gz read4PairFiles=M S1 L001 I2 001.fastq.gz	M_S1_L001_I1_001.fastq.gz M_S1_L001_I2_001.fastq.gz M_S1_L001_R1_001.fastq.gz M_S1_L001_R2_001.fastq.gz	fastq fastq fastq fastq	10297935498.0	74622721.0	GSM6956592 r1	0:28 1:90 2:10 3:10	A:2422395373;C:2014936837;G:2115011813;T:2251686635;N:1450420	28	90	10	10	2422395373	2014936837	2115011813	2251686635	1450420	SRX19140398	SRS16550346	SRA1578143	Department of Pharmacology, Yamagata University	Department of Pharmacology, Yamagata University	2	0.01687	0.92938	0.00583	0.17709	0.98549	0.82603	0.28254	0.55599	28	90	T	B	sc-like readlen	illumina	nextseq	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x		Japan	2023-01-22	Multi-stage	Multi-stage	Heart	Cardiovascular System