{"database": "metadata", "table": "run_metadata", "rows": [[66207, "SRR16097999", "SRX12384068", "SRS10354360", "SRP339110", "PRJNA767032", "Amino acid primed mTOR activity is essential for heart regeneration [scRNA seq]", "GSE184914", "Transcriptome Analysis", "Heart disease is the leading cause of death as there is no current method to repair damaged myocardium due to the limited proliferative capacity of adult cardiomyocytes.  Curiously  mouse neonates and zebrafish  larvae or adult  are able to regenerate their hearts via cardiomyocyte de differentiation and proliferation.  However  a molecular mechanism of why these cardiomyocytes can re enter cell cycle is poorly understood.  Here  we identify a unique metabolic state that primes adult zebrafish and neonatal mouse ventricular cardiomyocytes to proliferate.  Zebrafish and neonatal mouse hearts display elevated glutamine levels  predisposing them to amino acid driven activation of TOR. We show that this TOR activation is required for zebrafish cardiomyocyte regeneration in vivo. post injury we observe pS6 in both the epicardium and ventricular cardiomyocytes suggesting these are amino acid primed cells necessary for regeneration. Through single cell and system wide RNA sequencing  LQC proteomics and microscopy we identify dramatic metabolic and mitochondrial changes during the first week of regeneration. These data suggest that regeneration of zebrafish myocardium is driven by metabolic remodeling and reveals a unique metabolic regulator  TOR primed state  in which zebrafish and mammalian cardiomyocytes are regeneration competent. Overall design: We performed single cell RNA seq of zebrafish heart pre injury  and 3  7 xxx post injury", "parent bioproject:PRJNA778001", "pubmed:34988408", null, "zebrafish day 7", "GSM5600324", null, "source name:Zebrafish heart|tissue:heart|strain:AB|time:xxx post injury", "zebrafish day 7", "Raw reads were processed using the CellRanger software from 10X genomics using recommended default settings. Monocle version 3 alpha was used for single cell RNA seq data analysis and visualization. We kept cells with at least 200 expressed genes  and 1000 Unique Molecular Identifiers UMIs  and less than 40% reads mapped to mitochondrial transcripts. Genome build: GRCz10 Supplementary files format and content: tab delimited file of normalized gene level read counts for each cell", "Zebrafish heart", "All chemical ventricular cardiomyocyte VCM ablation were conducted on adult Zebrafish 5 mpf 12 mpf. For chemical mediated VCM ablation  fish were treated with 5 mM Metronidiazole MTZ; Sigma containing 0.1% dimethyl sulfoxide DMSO or vehicle control 0.1% DMSO for 48 hours protected from light and refreshed every 24 hours. For Wnt and DKK heat shock heterozygous animals  7.5 mM MTZ was used.  Following chemical treatment fish were placed back in original aquaria and hearts were collected at 0 prior to MTZ  3  7  12 and 30 xxx post injury dpi. Larval hearts 72 hpf were isolated and pooled as previously described [68  69]. 6 hearts  3 males and 3 females  were isolated from Adult UI  3 dpi and 7 dpi zebrafish.  Each group had 2 sets of samples of 3 hearts each for the digestion process.  Each set of 3 hearts were single celled as previously described [79].  All cells per group were then pooled and sent for sequencing.", "Cells were resuspended in PBS containing 0.04% BSA at a concentration of 2600 cells/ 33.8 \u03bcL solution. In total  2600 cells per sample were loaded into each well of a 10X Chromium single cell capture chip with a recovery of 272 cells for uninjured heart  141 cells for 3 xxx post injury and 368 cells for 7 xxx post injury sample. The captured cells then underwent lysis  reverse transcription  cDNA amplification  and library preparation with indexing per the manufacturer\u2019s protocol 10X Genomics. The libraries were sequenced together on an Illumina HiSeq 4000 Illumina Inc.  San Diego  CA using a high output 150 cycle kit with read lengths recommended by 10X Genomics.", "Wild type AB; Zebrafish International Resource Center  Eugene  OR  USA    hsWnt8:GFP [Tghsp70l:Wnt8a GFPw34] and hsDKK1:GFP [Tghsp70l:DKK1b GFPw32] [19] and vmhc:mCherry NTR [Tgvmhc:mCherry Eco.NfsB] [5] were used and maintained using standard procedures [67] in accordance with the Institutional Animal Care and Use Committee approved protocols IACUC 2057 01 & 4364 02. Reverse osmosis system water is used and the water chemistry was adjusted to a temperature of 27.5\u00b0C  pH of 7.5  conductivity of 800 \u00b5S  hardness of 140 ppm  alkalinity of 35 ppm  dissolved oxygen content of 7.8 mg/L  and a total gas pressure of 101%. The average nitrate level is 55 ppm  the average nitrite level is 0.05 ppm  and the average ammonium level is 0.01 ppm. Larval feed starting at 5 dpf dpf is a rotifer polyculture supplemented with the Zeigler larval diet  at 12 dpf live artemia is added to the diet  and at 60 dpf 90 dpf the fish are started on the Zeigler adult diet supplemented with live artemia once per day. The health status of the colony showed low presence of pseudoloma neurophilia and an extremely low presence of mycobacterium spp. with no major clinical or subclinical findings of significance.", "tissue:heart|strain:AB|time:xxx post injury", "GSM5600324", "GSM5600324: zebrafish day 7; Danio rerio; RNA Seq", "GSM5600324 r1", "GSM5600324", "1", "Cells were resuspended in PBS containing 0.04% BSA at a concentration of 2600 cells/ 33.8 \u03bcL solution. In total  2600 cells per sample were loaded into each well of a 10X Chromium single cell capture chip with a recovery of 272 cells for uninjured heart  141 cells for 3 xxx post injury and 368 cells for 7 xxx post injury sample. The captured cells then underwent lysis  reverse transcription  cDNA amplification  and library preparation with indexing per the manufacturer's protocol 10X Genomics. The libraries were sequenced together on an Illumina HiSeq 4000 Illumina Inc.  San Diego  CA using a high output 150 cycle kit with read lengths recommended by 10X Genomics.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP339110", null, "assembly:GRCz10|intentional duplicate", "zf_7db_possorted_genome_bam.bam", "10X Genomics bam file", 38062513314.0, 388392993.0, "GSM5600324 r1", "0:98", "A:11679656809;C:7784611418;G:8037807349;T:10544896124;N:15541614", 98, null, null, null, 11679656809, 7784611418, 8037807349, 10544896124, 15541614, "SRX12384068", "SRS10354360", "SRA1301815", "Institute for Stem Cell and Regenerative Medicine", "Institute for Stem Cell and Regenerative Medicine", 1, 0.93286, null, 0.08896, null, 0.87237, null, 0.56993, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2021-09-28", "Multi-stage", "Multi-stage", "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": ["66207"], "units": {}, "query_ms": 9.778703999472782}