{"database": "metadata", "table": "run_metadata", "rows": [[72826, "SRR23190065", "SRX19140397", "SRS16550345", "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/\u00df catenin signaling activated cardiomyocytes \u00df cat ON CMs promote coronary vessel development  we performed single cell RNA sequencing of endothelial cells ECs sorted from the hearts ablated \u00df cat ON CMs and those from control hearts  respectively. Our analyses indicated that \u00df 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 \u00df 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", null, "EC  DMSO  scRNAseq", "GSM6956591", null, "source name:Heart|tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP  myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry|cell type:Endothelial cells|treatment:DMSO", "EC  DMSO  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 TCF\u0394C;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 \u00baC. post pipetting  the cells were collected into low binding tubes  pelleted 3000 rpm  5 min at 4\u00baC  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\u2019reagent kits v3.1 10X Genomics  1000128  according to the manufacturer\u2019s 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.", null, "tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP  myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry|cell type:Endothelial cells|treatment:DMSO", "GSM6956591", "GSM6956591: EC  DMSO  scRNAseq; Danio rerio; RNA Seq", "GSM6956591 r1", "GSM6956591", "1", "Hearts were resected from Tgfli1:EGFP;Tgmyl7:GAL4db TCF\u0394C;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 \u00baC. post pipetting  the cells were collected into low binding tubes  pelleted 3000 rpm  5 min at 4\u00baC  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.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP418629", null, "loader:fastq load.py|options:  readTypes=BBTT   read1PairFiles=D S1 L004 R1 001.fastq.gz   read2PairFiles=D S1 L004 R2 001.fastq.gz   read3PairFiles=D S1 L004 I1 001.fastq.gz   read4PairFiles=D S1 L004 I2 001.fastq.gz", "D_S1_L004_I1_001.fastq.gz D_S1_L004_I2_001.fastq.gz D_S1_L004_R1_001.fastq.gz D_S1_L004_R2_001.fastq.gz", "fastq fastq fastq fastq", 10731126882.0, 77761789.0, "GSM6956591 r4", "0:28 1:90 2:10 3:10", "A:2577638514;C:2068754148;G:2196571470;T:2332228096;N:698874", 28, 90, 10, 10, 2577638514, 2068754148, 2196571470, 2332228096, 698874, "SRX19140397", "SRS16550345", "SRA1578143", "Department of Pharmacology, Yamagata University", "Department of Pharmacology, Yamagata University", 2, 0.01687, 0.9273, 0.00577, 0.18031, 0.98476, 0.82954, 0.28103, 0.55337, 28, 90, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Japan", "2023-01-22", "Multi-stage", "Multi-stage", "Heart", "Cardiovascular System"]], "columns": ["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"], "primary_keys": ["rowid"], "primary_key_values": ["72826"], "units": {}, "query_ms": 14.511083994875662}