{"database": "metadata", "table": "run_metadata", "rows": [[73907, "SRR23290111", "SRX19233404", "SRS16637863", "SRP420294", "PRJNA929922", "Cloche is a pro regenerative platelet factor during zebrafish heart regeneration [10x scRNA seq]", "GSE224111", "Transcriptome Analysis", "Zebrafish heart regeneration is a complex process consisting of tempo spatial coordination of cardiomyocyte CM and endothelial cell EC regeneration  fibrosis and inflammation. While myocardial  endocardial  and epicardial signaling have been reported to modulate this process  little is known about how leukocyte especially platelet signaling is involved in this regenerative process. Here we report that cloche/npas4l neuronal PAS domain protein 4 like is a pro regenerative platelet factor for adult zebrafish heart regeneration. We found that injury triggered npas4l expression as early as 1 h post ventricular amputation  and haploinsufficiency of npas4l disrupted CM and EC proliferation and heart regeneration in clofv087b/+ and clom39/+ mutants post ventricular resection or nitroreductase NTR mediated CM ablation. By constructing a single cell transcriptomic atlas  we discovered that npas4l was dynamically expressed in platelets in response to heart injury with robust platelet CM or  EC interactions via ligand receptor activity analysis. Decreasing platelets in NTR mediated depletion or mpl mutants impaired CM and EC proliferation  and over expression of npas4l in platelets sufficiently made uninjured and injured CM reentry into the cell cycle and rescued CM and EC proliferation in clofv087b/+ mutants. Furthermore  Npas4l positively regulated Bmp6 expression in platelets and either BMP6 inhibitors or siRNAs decreased CM proliferation and heart regeneration. This work demonstrates  for the first time  that injury induced platelets are essential for zebrafish heart regeneration and Npas4l is a core platelet transcription factor for fine tuning heart regeneration partially via Bmp6 signaling. Overall design: Wild type and clofv087b/+ adult zebrafish hearts injured or uninjured were dissected and cardiac cells were disassociation at 4?. Fluorescence activated cell sorting FACS was used to remove cell debris and sort for single cell according to hochest signal intensity. Sorted cell concentration and vaibility were determined on a Countstar Rigel system. 12 000 cells with more than 85% cell vaibility were loaded into 10x Genomics Chromium chip and proceeded to single cell RNA library construction and sequencing.", "parent bioproject:PRJNA929937", null, null, "clofv087b/+ 7dpa", "GSM7012026", null, "source name:heart|tissue:heart|cell line:isolated primary cells|cell type:cardiac cells|genotype:clofv087b/+|treatment:7 dy post heart amputation|geo loc name:missing|collection date:missing", "clofv087b/+ 7dpa", "Illumina Casava2.1.7 software used for basecalling. Cell Ranger v3.0.2 pipeline 10x Genomics was utilized to demultiplex the cellular barcodes and align reads to the GRCz11 zebrafish reference genome. The output filtered gene expression matrices were loaded and analyzed using the Seurat package v3.1.4 Potential doublet cells were detected and filtered using the R package DoubletFinder v2.0.2 Low quality cells were removed from the datasets based on the following criteria: 1 the number of detected genes <=200 or >=4 000  the percentage of mitochondrial genes >=25 for non cardiomyocytes; 2 the number of detected genes <=200 or >=4 000 for CMs  the mitochondrial content was not filtered due to the nature of CMs containing high mitochondrial density Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files", "heart", null, "For each sample  15 adult ventricles were collected and placed in ice cold perfusion buffer 130 mM NaCl  5 mM KCl  0.5 mM NaH2PO4  10 mM HEPES  10 mM Glucose  10 mM 2 3 butanedionemonoxime  10 mM taurine  5 mM MgCl2  adjusting pH to 7.8 with NaOH. The ventricles were gently torn up  transferred  and digested in the digestion buffer 10 mg/ml protease  30 \u03bcg/ml DNase I in perfusion buffer for 3 h at 4\u2103 with constant gentle agitation by using a rotator. The digestion was then neutralized with 10% FBS fetal bone serum and the disassociated cells were filtered through a 100 \u03bcm strainer to remove large clumps and pelleted at 500 x g for 10 min at 4\u2103. The pellet was re suspended in Hank\u2019s balance salt solution HBSS. The disassociated cells were stained with Hochest 33342 1:300 diluted in HBSS   gone through a 70 \u03bcm strainer  and loaded on a Beckman Coulter MoFlo XDP system to remove cell debris and sort for single cells. The sorted single cells were pelleted at 1000 x g for 5 min at 4\u2103. The pellet was resuspended in HBSS. Cell viability and concentration were measured on a Countstar Rigel system ALIT Life Science. Samples with more than 85% cell viability were qualified for single cell loading. Around 12 000 cells per sample were loaded into 10x Genomics Chromium chip. Single cell RNA seq libraries were generated using Chromium Next GEM Single Cell 3\u2019 Kit v3.1 10x Genomics  1000269 according to the manufacturer\u2019s instructions.", null, "tissue:heart|cell line:isolated primary cells|cell type:cardiac cells|genotype:clofv087b/+|treatment:7 dy post heart amputation", "GSM7012026", "GSM7012026: clofv087b/+ 7dpa; Danio rerio; RNA Seq", "GSM7012026 r1", "GSM7012026", "1", "For each sample  15 adult ventricles were collected and placed in ice cold perfusion buffer 130 mM NaCl  5 mM KCl  0.5 mM NaH2PO4  10 mM HEPES  10 mM Glucose  10 mM 2 3 butanedionemonoxime  10 mM taurine  5 mM MgCl2  adjusting pH to 7.8 with NaOH. The ventricles were gently torn up  transferred  and digested in the digestion buffer 10 mg/ml protease  30 \u03bcg/ml DNase I in perfusion buffer for 3 h at 4\u2103 with constant gentle agitation by using a rotator. The digestion was then neutralized with 10% FBS fetal bone serum and the disassociated cells were filtered through a 100 \u03bcm strainer to remove large clumps and pelleted at 500 x g for 10 min at 4\u2103. The pellet was re suspended in Hank's balance salt solution HBSS. The disassociated cells were stained with Hochest 33342 1:300 diluted in HBSS   gone through a 70 \u03bcm strainer  and loaded on a Beckman Coulter MoFlo XDP system to remove cell debris and sort for single cells. The sorted single cells were pelleted at 1000 x g for 5 min at 4\u2103. The pellet was resuspended in HBSS. Cell viability and concentration were measured on a Countstar Rigel system ALIT Life Science. Samples with more than 85% cell viability were qualified for single cell loading. Around 12 000 cells per sample were loaded into 10x Genomics Chromium chip. Single cell RNA seq libraries were generated using Chromium Next GEM Single Cell three prime Kit v3.1 10x Genomics  1000269 according to the manufacturer's instructions.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP420294", null, "loader:fastq load.py", "het_7dpa_S1_L001_R1_001.fastq.gz het_7dpa_S1_L001_R2_001.fastq.gz", "fastq fastq", 260015683500.0, 866718945.0, "GSM7012026 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX19233404", "SRS16637863", "SRA1583282", "Tsinghua University", "Tsinghua University", 2, 0.02577, 0.921, 0.00416, 0.12938, 0.99825, 0.81633, 0.65925, 0.48986, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2023-01-31", "Adult", "Adult", "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": ["73907"], "units": {}, "query_ms": 10.998960999131668}