{"database": "metadata", "table": "run_metadata", "rows": [[56965, "SRR11186423", "SRX7806757", "SRS6219792", "SRP250826", "PRJNA608913", "Single cell analysis of non myocytes during heart regeneration reveals sequential coordinated responses from distinct cell populations [bulk RNA seq]", "GSE145979", "Transcriptome Analysis", "Cardiac regeneration occurs primarily through proliferation of existing cardiomyocytes  yet the regenerative response also involves complex interactions between distinct cardiac cell types including not only cardiomyocytes  but also non cardiomyocytes nonCMs. However  the molecular features and cellular functions of the highly heterogeneous populations of nonCMs and how these populations cooperate to regenerate the injured heart remain largely unexplored. Using the newly developed LIGER algorithm that allows flexible modeling across highly diverse single cell datasets  we analyzed the transcriptome dynamics of 61 977 individual nonCMs isolated at multiple time points during zebrafish heart regeneration. Combining single cell analysis and in situ hybridization  we identified major nonCM cell types  including multiple novel subpopulations with unique tempo spatial distributions and highly cooperative interactions in the regenerating heart. Interestingly  genetic perturbation of macrophage function by kit knockout led to accumulation of fibrotic deposits and severely compromised cardiomyocyte proliferation and myocardium regeneration. Our single cell transcriptomic analysis of nonCMs during cardiac regeneration provides a blueprint for interrogating the molecular and cellular basis of cardiac regeneration. Overall design: To assess the proliferation defect of kit aka  c kit mutant CMs  we conducted transcriptome wide bulk RNA seq of control and mutant cardiomyocytes", "parent bioproject:PRJNA608906", "pubmed:34523214", null, "zCM kit 5dpi2", "GSM4340632", null, "source name:zCM kit 5dpi|genotype/variation:kit mutant; kitaw34b2;kitbsa15356|treatment/timepoint:5 xxx post injury|age:4 month 6 month|tissue:heart|cell type:cardiomyocytes", "zCM kit 5dpi2", "Qualities of de barcoded raw sequence reads were checked by fastqc. The alignment was performed using BBMap/38.1213 against the reference zebrafish genome UCSC DanRer10 Gene counts were obtained using featureCounts. The raw counts were normalized to sequencing depth using counts per million CPM. Genome build: UCSC DanRer10 Supplementary files format and content: tab delimited text files containing CPM values for each sample", "zCM kit 5dpi", "Zebrafish were anesthetized by immersion with 0.04% tricaine and immobilized in a dampened foam with ventral side up. A small incision was made between the gills to expose the ventricle. About 20% of ventricular apex was resected using iridectomy scissors. post apex resection  fish were returned to a recovery tank with fresh system water.", "Total RNAs of isolated adult zebrafish cardiomyocytes from eight pooled ventricles were extracted using QIAGEN RNeasy Micro kit. Illumina libraries were prepared using TrueSeq Standard mRNA Sample Preparation Kit.", "Zebrafish were raised and maintained under standard laboratory conditions.", "genotype/variation:kit mutant; kitaw34b2;kitbsa15356|treatment/timepoint:5 xxx post injury|age:4 month 6 month|tissue:heart|cell type:cardiomyocytes", "GSM4340632", "GSM4340632: zCM kit 5dpi2; Danio rerio; RNA Seq", "GSM4340632", null, "1", "Total RNAs of isolated adult zebrafish cardiomyocytes from eight pooled ventricles were extracted using QIAGEN RNeasy Micro kit. Illumina libraries were prepared using TrueSeq Standard mRNA Sample Preparation Kit.", "GEO Accession:GSM4340632", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP250826", null, null, "Z5DPI-2-z5dpi-2_AGTTCC_S31_L008_R2_001.fastq.gz Z5DPI-2-z5dpi-2_AGTTCC_S31_L008_R1_001.fastq.gz", "fastq fastq", 4536186100.0, 45361861.0, "GSM4340632 r1", "0:50 1:50", "A:1229515994;C:1008510173;G:1046866818;T:1249817681;N:1475434", 50, 50, null, null, 1229515994, 1008510173, 1046866818, 1249817681, 1475434, "SRX7806757", "SRS6219792", "SRA1048426", "GEO", "University of North Carolina at Chapel Hill", 2, 0.94703, 0.94916, 0.04052, 0.03996, 0.79299, 0.79498, 0.65851, 0.61547, 50, 50, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2020-02-26", "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": ["56965"], "units": {}, "query_ms": 7.750967997708358}