{"database": "metadata", "table": "run_metadata", "rows": [[31528, "SRR28423881", "SRX24027916", "SRS20821688", "SRP497294", "PRJNA1090898", "The innate immune regulator MyD88 dampens fibrosis during zebrafish heart regeneration dst169", "GSE262247", "Transcriptome Analysis", "The innate immune system is triggered xxx post injury and its spatiotemporal dynamics are critical for successful regeneration.  MyD88 is a key component of the innate immune response; however  its role during regeneration remains unclear.  Here we show that MyD88 controls not only the inflammatory but also the fibrotic response during zebrafish cardiac regeneration.  Our data reveal a significant reduction in pro inflammatory neutrophil and macrophage populations  as well as the expansion of a collagen rich endocardial population in cryoinjured myd88 /  ventricles.  Consistent with these findings  we observed increased myofibroblasts  fibrin abundance  and scarring in myd88 /  ventricles.  Transcriptomic analyses of endocardial cells and immunostaining experiments reveal compromised PI3K/AKT pathway activation in the myd88 /  endocardium.  Moreover  loss of MyD88 impairs cardiomyocyte proliferation and protrusive activity towards the injured area.  Notably  endothelial specific overexpression of myd88 reverses the neutrophil  fibrotic  and scarring phenotypes in cryoinjured myd88 /  ventricles.  Mechanistically  we identify the endocardial derived chemokine gene cxcl18b as a transcriptional target of the MyD88 signaling axis and using loss  and gain of function tools show that it controls neutrophil recruitment.  Altogether  these findings shed light on the pivotal role of MyD88 in modulating inflammation and fibrosis  thereby emphasizing the strong impact of the innate immune response during tissue regeneration. Overall design: Live zebrafish ventricular cells were isolated at 24 hour post cryoinjury hpci from myd88+/+ and myd88 /  ventricles by Fluorescence activated cell sorting FACS and analyzed using scRNAseq.", "parent bioproject:PRJNA1090894", "pubmed:39271818", null, "ventricular cells  myd88 /   24 hpci", "GSM8161054", null, "source name:cardiac ventricles|tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88 / |treatment:cardiac cryoinjury|geo loc name:missing|collection date:missing", "ventricular cells  myd88 /   24 hpci", "Raw reads were aligned against the zebrafish genome DanRer11 and counted by StarSolo Dobin et al.  doi: 10.1093/bioinformatics/bts635 followed by secondary analysis in Annotated Data Format. Preprocessed counts were further analyzed using Scanpy Wolf et al.  doi: 10.1186/s13059 017 1382 0. Basic cell quality control was conducted by taking the number of detected genes and mitochondrial content into consideration. We removed 32 cells in total that did not express more than 300 genes or had a mitochondrial content greater than 10%. Furthermore  we filtered 7823 genes if they were detected in less than 30 cells <0.01%. Raw counts per cell were normalized to the median count over all cells and transformed into log space to stabilize variance We initially reduced dimensionality of the dataset using PCA  retaining 50 principal components. Subsequent steps  like low dimensional UMAP embedding McInnes & Healy  https://arxiv.org/abs/1802.03426 and cell clustering via community detection Traag et al.  https://arxiv.org/abs/1810.08473  were based on the initial PCA. Final data visualization was done by CellxGene package DOI 10.5281/zenodo.3235020. Assembly: DanRer11 Supplementary files format and content: starsolo outputs", "cardiac ventricles", "cardiac cryoinjury 24 hours prior to heart extraction", "Ventricular cells were isolated from a pool of 4 myd88+/+ and 4 myd88 /  ventricles for the myd88+/+ and myd88 /  sample  respectively. Cell isolation was performed with the Pierce Primary Cardiomyocyte Isolation Kit Thermo Fisher Scientific following the manufacturer\u2019s instructions and with the following modifications: Incubation was performed at 30\u00b0C for 20 min  followed by resuspension in 1\u00d7 Hanks\u2019 balanced salt solution Gibco with 0.25% BSA. Suspended cells were sorted using FACSAriaIII sorter BD to exclude dead cells using DAPI Sigma. Library preparation was conducted according to the manufacturer indications Chromium Next GEM Single Cell 3\u2019 GEM  Library & Gel Bead Kit v3.1  16 rxns PN 1000121.", null, "tissue:cardiac ventricles|cell type:ventricular cells|genotype:myd88 / |treatment:cardiac cryoinjury", "GSM8161054", "GSM8161054: ventricular cells  myd88 /   24 hpci; Danio rerio; RNA Seq", "GSM8161054 r1", "GSM8161054", "1", "Ventricular cells were isolated from a pool of 4 myd88+/+ and 4 myd88 /  ventricles for the myd88+/+ and myd88 /  sample  respectively. Cell isolation was performed with the Pierce Primary Cardiomyocyte Isolation Kit Thermo Fisher Scientific following the manufacturer's instructions and with the following modifications: Incubation was performed at 30\u00b0C for 20 min  followed by resuspension in 1\u00d7 Hanks' balanced salt solution Gibco with 0.25% BSA. Suspended cells were sorted using FACSAriaIII sorter BD to exclude dead cells using DAPI Sigma. Library preparation was conducted according to the manufacturer indications Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1  16 rxns PN 1000121.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP497294", null, null, "Pinelopi_10x_Zebrafish_Mut_Lib_R1.fastq.gz Pinelopi_10x_Zebrafish_Mut_Lib_R2.fastq.gz", "fastq fastq", 31356990530.0, 394538049.0, "GSM8161054 r1", "0:28 1:51.48", "A:8573180857;C:6884590114;G:7520784498;T:8220228225;N:158206836", 28, 51, null, null, 8573180857, 6884590114, 7520784498, 8220228225, 158206836, "SRX24027916", "SRS20821688", "SRA1832827", "MPI for heart and lung research", "MPI for heart and lung research", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "nextseq_v2", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2024-03-22", "Cleavage", "Embryo", "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": ["31528"], "units": {}, "query_ms": 7.587252999655902}