{"database": "metadata", "table": "run_metadata", "rows": [[69529, "SRR22489947", "SRX18455101", "SRS15933713", "SRP371323", "PRJNA828542", "RNA seq experiments on heart regeneration in WT  foxm1 and dusp6 mutants.", "GSE201139", "Transcriptome Analysis", "The study compares gene expression profile at several stages post amputation of the adult zebrafish ventricular heart between zebrafish mutants and WT siblings. The first experiment was to identify genes that are activated in response to cardiac injury at 3 and 7 dy post amputation dpa. Dusp6 mutant hearts were reported to show an enhanced regenerative response. For this experiment  bulk RNA seq was obtained from WT and Dusp6 mutant hearts and genes increased at 3 and 7 dpa were identified. The forkhead transcription factor  foxm1  showed increased expression in cardiomyocytes and follow up studies show that it is required to regulate cardiomyocyte proliferation. This was further explored with RNA seq experiments comparing WT and foxm1 mutant hearts at 3dpa. We identified genes normally expressed in proliferating cells to be decreased in the foxm1 mutants. Overall design: Ventricular resection was performed on WT  dusp6 and foxm1 mutant hearts. Uninjured adult hearts were used as control to compare to hearts at 3 and 7 dy post amputation dpa.", null, "pubmed:36846912", null, "WT heart 7dpa", "GSM6775412", null, "source name:Heart|tissue:Heart|genotype:AB*|time point:7dpa", "WT heart 7dpa", "fastq files were analyzed using CLC genomics workbench 20.0 sequence reads were mapped onto Danio rerio GRC.z11 EDGE test was performed using CLC genomics workbench Assembly: Danio rerio GRC.z11 Supplementary files format and content: Zuppo et al 7dpa vs. uninj.xlsx", "Heart", null, "Adutls hearts were injured through ventricular resection and allowed to recover until 7 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|genotype:AB*|time point:7dpa", "GSM6775412", "GSM6775412: WT heart 7dpa; Danio rerio; RNA Seq", "GSM6775412 r1", "GSM6775412", "1", "Adutls hearts were injured through ventricular resection and allowed to recover until 7 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", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP371323", null, null, "Wt_1-2_Wt2_7dpa_S1_R1_001.fastq.gz", "fastq", 12872883182.0, 85250882.0, "GSM6775412 r1", "0:151 1:0", "A:3575062004;C:2980475677;G:2968169651;T:3348722223;N:453627", 151, 0, null, null, 3575062004, 2980475677, 2968169651, 3348722223, 453627, "SRX18455101", "SRS15933713", "SRA1550906", "Developmental Biology, University of Pittsburgh", "Developmental Biology, University of Pittsburgh", 1, 0.89153, null, 0.07646, null, 0.75948, null, 0.50786, null, 151, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-12-01", "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": ["69529"], "units": {}, "query_ms": 10.921556000539567}