{"database": "metadata", "table": "run_metadata", "rows": [[33716, "SRR30621746", "SRX26043962", "SRS22614938", "SRP531880", "PRJNA1159283", "Nr4a1 Modulates Inflammation and Heart Regeneration in Zebrafish", "GSE276850", "Transcriptome Analysis", "Recent findings have highlighted the complex role of inflammation in zebrafish heart regeneration  demonstrating that while inflammation is essential for initiating transient fibrosis and tissue repair  chronic inflammation and unresolved fibrosis could impede full regenerative recovery. In this study  we identified the nuclear receptor Nr4a1 as a critical regulator of this regenerative process in zebrafish. Loss of Nr4a1 function led to a prolonged and excessive inflammatory response  disrupted neutrophil migration  delayed fibrin clearance  and ultimately impaired heart regeneration. Transcriptome wide RNA seq analysis at different injury stages revealed molecular disruptions associated with dysregulated inflammation and fibrosis in Nr4a1 mutants. Notably  partial inhibition of the pro inflammatory cytokine Tnf a rescued heart regeneration in the nr4a1 mutants  highlighting the therapeutic potential of modulating inflammation. Our findings suggest that Nr4a1 plays a crucial role in orchestrating the immune response during heart regeneration and may serve as a valuable target for enhancing cardiac repair following injury. Overall design: To elucidate the molecular basis of the phenotypes observed in the nr4a1 mutant  we performed transcriptome wide bulk RNA sequencing on the ventricles from both control and mutant hearts at several key time points. Baseline transcriptomic profiles were established from uninjured hearts to compare the cardiac transcriptomics of the wildtype control and nr4a1 mutant. Given the critical involvement of inflammation in heart regeneration  samples were also collected at 2 and 7 dpci  corresponding to stages marked by an active inflammatory response. Moreover  to elucidate the prolonged fibrosis phenotype in the late injury stage  we performed transcriptomic analysis on hearts collected at 21 dpci.", null, null, null, "nr4a1 mutant 7 dpi sample 2", "GSM8506773", null, "source name:Heart ventricle|tissue:Heart ventricle|genotype:nr4a1 mutant|geo loc name:missing|collection date:missing", "nr4a1 mutant 7 dpi sample 2", "RNA seq raw data quality was checked by FastQC https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. RNA seq were aligned to the zebrafish reference genome using STARDobin et al.  2013. Gene expression was quantified as gene hit counts reads per gene using FeatureCountsLiao et al.  2014. Assembly: Danio rerio zebrafish genome assembly GRCz11 danRer11 Supplementary files format and content: txt data file include raw counts for each sample", "Heart ventricle", null, "Total RNA was isolated from zebrafish ventricles using Trizol Invitrogen. Reverse transcription was performed using SuperScript IV VILO Master Mix Invitrogen. For RNA seq  library preparation and Illumina RNA seq were performed by Novogene.", null, "tissue:Heart ventricle|genotype:nr4a1 mutant", "GSM8506773", "GSM8506773: nr4a1 mutant 7 dpi sample 2; Danio rerio; RNA Seq", "GSM8506773 r1", "GSM8506773", "1", "Total RNA was isolated from zebrafish ventricles using Trizol Invitrogen. Reverse transcription was performed using SuperScript IV VILO Master Mix Invitrogen. For RNA seq  library preparation and Illumina RNA seq were performed by Novogene.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq X Plus", null, "SRP531880", null, null, "nr4a1_7dpi_2_1.fq.gz nr4a1_7dpi_2_2.fq.gz", "fastq fastq", 5512600871.0, 18517476.0, "GSM8506773 r1", "0:148.84 1:148.85", "A:1483061100;C:1285068800;G:1269689220;T:1474711048;N:70703", 148, 148, null, null, 1483061100, 1285068800, 1269689220, 1474711048, 70703, "SRX26043962", "SRS22614938", "SRA1968119", "The University of North Carolina", "The University of North Carolina", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2024-09-10", "Undetermined", "Undetermined", "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": ["33716"], "units": {}, "query_ms": 9.135713000432588}