{"database": "metadata", "table": "run_metadata", "rows": [[55248, "SRR10203906", "SRX6923951", "SRS5454833", "SRP223736", "PRJNA575000", "\u00adrunx1 controls zebrafish heart regeneration by promoting scar deposition as well as inhibiting myocardial proliferation and survival", "GSE138181", "Transcriptome Analysis", "Runx1 is a transcription factor that plays a key role in determining the proliferative and differential state of multiple cell types  during both development and maturity. Here  we report how runx1 is specifically upregulated at the injury site during zebrafish heart regeneration  but unexpectedly  absence of runx1 results in enhanced regeneration. Using single cell sequencing  we found that the wild type injury site consists of Runx1 positive endocardial cells and thrombocytes that express smooth muscle and collagen genes without xxx into myofibroblasts. Both these populations are absent in runx1 mutants  resulting in a less collagenous and fibrinous scar. The reduction in fibrin in the mutant is further explained by reduced myofibroblast formation and by upregulation of components of the fibrin degradation pathway  including plasminogen receptor Annexin 2A as well as downregulation of plasminogen activator inhibitor serpine1 in myocardium and endocardium  resulting in increased levels of Plasminogen. In addition  this we also find enhanced myocardial proliferation as well as increased myocardial survival in the mutant. Our findings suggest that Runx1 controls the regenerative response of multiple cardiac cell types and that targeting Runx1 is a novel therapeutic strategy to induce endogenous heart repair. Overall design: To determine the differences between wild type  wild type injured and wild type runx1 KO runx1+ endothelial cells in Zebrafish", null, "pubmed:32341028", null, "587680 45", "GSM4101380", null, "source name:Uninjured Wild Type|tissue:Heart Ventricle pool 20 hearts|strain:KCL|genotype:WT|treatment:uninjured", "587680 45", "Reads aligned to Danio rerio.GRCz11 release 94 and processed using Cell Ranger v2.1.1 Counts extracted using scanpy in python Genome build: Danio rerio.GRCz11 release 94 Supplementary files format and content: Counts: Mapped read counts per gene  per cell", "Uninjured Wild Type", "A small incision was made through the thorax and the pericardium using forceps and spring scissors. The abdomen was gently squeezed to expose the ventricle and tissue paper was used to dry the heart. A cryo probe with a copper filament was cooled in liquid nitrogen and placed on the ventricle surface until thawing was observed. Body wall incisions were not sutured  and post surgery  fish were returned to water and stimulated to breathe by pipetting water over the gills until the fish started swimming again. For sham surgery  the thorax and pericardial sac were opened  but the heart was not injured. All operated fish were kept in individual tanks for the first week post surgery  then fish were combined in larger tanks.", "Hearts were extracted and transferred to Ringer solution with heparin sodium salt 50 U/ml Ringer composition: 7.2 g NaCl  0.225g CaCl2.H2O  0.37 g KCl  0.2175g Na2HPO4.7H2O  0.02g KH2PO4 at pH 7.4 sterilized by using a 0.22um bottle top filter unit and rinsed once with Phosphate buffered saline PBS or directly isolated in PBS. Hearts were inspected  cleaned and then fixed with 4% Paraformaldehyde PFA overnight O/N on nutator at room temperature RT. Samples were rinsed once in PBS  dehydrated into Ethanol EtOH at 70%  80%  90%  96%  for 2 hours each step and 2x100% for 1 hour each step  followed by a 100% 1 butanol step overnight. The samples were then transferred to paraffin Paraplast Plus  Sigma Aldrich P3683 wax at 65\u00b0C. Cells were washed in PBS with 0.04% BSA and re suspended before loading 12 000 12 500 cells onto each channel of the Chromium 10x Genomics platform to capture single cells in droplets. Library generation for 10x Genomics v2 chemistry was performed following the Chromium Single Cell 3\u02b9 Reagents Kits User Guide: CG00052. Quantification of cDNA was performed using Qubit dsDNA HS Assay Kit Life Technologies Q32851 and high sensitivity DNA tape station Agilent. 5067 5584. Quantification of library construction was performed using Qubit dsDNA HS Assay Kit Life Technologies Q32851 and high sensitivity DNA tape station Agilent. 5067 5584.", "Adult wild type wt KCL strain  Tgkdrl:Hsa.HRAS mCherry34 subsequently referred to as Tgkdrl:mCherry and runx1W84X mutants27  TgBACrunx1P2:Citrine29  were housed in a Techniplast aquarium system [28\u2009\u00b0C  14/10\u2009hours light/dark cycle  fed 3x daily with dry food and brine shrimp]. All double transgenic lines on wild type or mutant background were generated by natural mating.", "tissue:Heart Ventricle  pool 20 hearts|strain:KCL|genotype:WT|treatment:uninjured", "GSM4101380", "GSM4101380: 587680 45; Danio rerio; RNA Seq", "GSM4101380", null, "1", "Hearts were extracted and transferred to Ringer solution with heparin sodium salt 50 U/ml Ringer composition: 7.2 g NaCl  0.225g CaCl2.H2O  0.37 g KCl  0.2175g Na2HPO4.7H2O  0.02g KH2PO4 at pH 7.4 sterilized by using a 0.22um bottle top filter unit and rinsed once with Phosphate buffered saline PBS or directly isolated in PBS. Hearts were inspected  cleaned and then fixed with 4% Paraformaldehyde PFA overnight O/N on nutator at room temperature RT. Samples were rinsed once in PBS  dehydrated into Ethanol EtOH at 70%  80%  90%  96%  for 2 hours each step and 2x100% for 1 hour each step  followed by a 100% 1 butanol step overnight. The samples were then transferred to paraffin Paraplast Plus  Sigma Aldrich P3683 wax at 65\u00b0C. Cells were washed in PBS with 0.04% BSA and re suspended before loading 12 000 12 500 cells onto each channel of the Chromium 10x Genomics platform to capture single cells in droplets. Library generation for 10x Genomics v2 chemistry was performed following the Chromium Single Cell 3\u02b9 Reagents Kits User Guide: CG00052. Quantification of cDNA was performed using Qubit dsDNA HS Assay Kit Life Technologies Q32851 and high sensitivity DNA tape station Agilent. 5067 5584. Quantification of library construction was performed using Qubit dsDNA HS Assay Kit Life Technologies Q32851 and high sensitivity DNA tape station Agilent. 5067 5584.", "GEO Accession:GSM4101380", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP223736", null, "loader:fastq load.py|options:  readTypes=TTB   read1PairFiles=587680 45 S60 L005 I1 001.fastq.gz   read2PairFiles=587680 45 S60 L005 R1 001.fastq.gz   read3PairFiles=587680 45 S60 L005 R2 001.fastq.gz", "587680_45_S60_L005_I1_001.fastq.gz 587680_45_S60_L005_R1_001.fastq.gz 587680_45_S60_L005_R2_001.fastq.gz", "fastq fastq fastq", 11134774992.0, 84354356.0, "GSM4101380 r1", "0:8 1:26 2:98", "A:3152110963;C:2379819000;G:2458427917;T:3139288192;N:5128920", 8, 26, 98, null, 3152110963, 2379819000, 2458427917, 3139288192, 5128920, "SRX6923951", "SRS5454833", "SRA969982", "GEO", "Haematology, University of Cambridge", 1, 0.90136, null, 0.13254, null, 0.84593, null, 0.51719, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2019-09-30", "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": ["55248"], "units": {}, "query_ms": 12.01882200257387}