{"database": "metadata", "table": "run_metadata", "rows": [[34065, "SRR31040097", "SRX26425362", "SRS22944827", "SRP539398", "PRJNA1174770", "cited4a limits CM dedifferentiation and proliferation during zebrafish heart regeneration [Bulk RNA seq]", "GSE279843", "Transcriptome Analysis", "Cardiac regeneration involves interplay of complex interactions between many different cell types  including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been under intense study. Here we report single nuclear RNA sequencing profile of the injured zebrafish heart and identified distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations indicate diverse functions that includes stress response  myofibril assembly  proliferation and contraction. The contracting cardiomyocyte population also involves activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this  we determined that cited4a  a p300/CBP transcriptional co activator  is xxx post injury in mature cardiomyocyte population. Moreover  loss of cited4a mutants showed increased dedifferentiation  proliferation and accelerated heart regeneration. Thus  suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration. Overall design: Wildtype and cited4a mutant adult heart regeneration study injured by ventricular amputation. Hearts were collected at 3 dy post amputation dpa. Total RNA was extracted from ventricles was used for RNA seq experiments.", null, "pubmed:39713454", null, "cited4a 2 S7", "GSM8581864", null, "source name:heart ventricle|tissue:heart ventricle|genotype:cited4a pt38a/pt38a|treatment:3 dpa|geo loc name:missing|collection date:missing", "cited4a 2 S7", "fastq files were processed with Cutadapt to remove adaptors Trimmed seq files were mapped to the zebrafish geneome using HiSat2 Mapped files were processed within featureCount for gene expression counts featureCount reads were imported into R package DeSeq2 for gene expression analysis. WT3 and cited4a 3 samples were omitted from the DeSeq2 analysis due to poor mapping. Normalized counts were calculated and log2 fold change and padj values were calculated using DeSeq2. Assembly: Danio rerio GRC.z11 Supplementary files format and content: RFR WTvsCited4aDeSeq2.xlsx Supplementary files format and content: .csv files are raw counts from featureCount processing post HiSat2 mapping.", "heart ventricle", null, "Adutls hearts were injured through ventricular resection and allowed to recover until 3 dy post amputation. Ventricles were removed  flash frozen on dry ice  and RNA was harvested using Trizol reagent and Quiagen RNeasy micro kit Cat# 74004.", "Zebrafish adult at 6 month  1year of age", "tissue:heart ventricle|genotype:cited4a pt38a/pt38a|treatment:3 dpa", "GSM8581864", "GSM8581864: cited4a 2 S7; Danio rerio; RNA Seq", "GSM8581864 r1", "GSM8581864", "1", "Adutls hearts were injured through ventricular resection and allowed to recover until 3 dy post amputation. Ventricles were removed  flash frozen on dry ice  and RNA was harvested using Trizol reagent and Quiagen RNeasy micro kit Cat# 74004.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP539398", null, null, "cited4a_2_S7_R1_001.fastq.gz cited4a_2_S7_R2_001.fastq.gz", "fastq fastq", 8918974871.0, 45257542.0, "GSM8581864 r1", "0:98.52 1:98.55", "A:2418106630;C:2024139848;G:2068607737;T:2389350414;N:18770242", 98, 98, null, null, 2418106630, 2024139848, 2068607737, 2389350414, 18770242, "SRX26425362", "SRS22944827", "SRA1993635", "Cell Biology, University of Pittsburgh", "Cell Biology, University of Pittsburgh", 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", "2024-10-18", "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": ["34065"], "units": {}, "query_ms": 7.773325000016484}