{"database": "metadata", "table": "run_metadata", "rows": [[62890, "SRR13426624", "SRX9841727", "SRS8023816", "SRP301573", "PRJNA691756", "Interspecies comparison reveals Hmga1 as a key determinator of cardiac regenerative potential", "GSE164729", "Transcriptome Analysis", "Myocardial infarction causes a massive loss of cardiomyocytes  leading to the formation of a fibrotic scar resulting in impaired cardiac function. In contrast to mammals  zebrafish display robust cardiac regeneration following injury due to the proliferation of pre existing cardiomyocytes in the injury border zone. Here  we aim to identify transcriptomic differences that will help explain the differential cardiac regenerative capacity observed between the injured zebrafish and mammalian heart. First  we transcriptionally profiled the border zone of the injured mouse heart  which does not support regeneration. Then  we bioinformatically compared the transcriptome of the mouse border zone with the zebrafish border zone  identifying many genes and processes overlapping or diverging between the two species. Interestingly  we identified the architectural chromatin remodeller hmga1a to be expressed in the zebrafish  but not the mouse border zone. Using a loss of function hmga1a mutant we show that hmga1a is required for border zone cardiomyocyte proliferation and zebrafish heart regeneration. Using single cell RNA sequencing  we identify the near absence of proliferative cardiomyocyte sub populations in hmga1a mutant border zones. Furthermore  we show that overexpression of hmga1a can induce cardiomyocyte proliferation in uninjured zebrafish hearts. Using a combination of RNA  and ATAC sequencing  we show that hmga1a overexpression leads to the induction of a broad border zone like gene program  including robust chromatin remodelling. Last  we provide evidence suggesting that overexpression of Hmga1 can stimulate mammalian cardiomyocyte proliferation and functional recovery post myocardial infarction. Taken together  through transcriptional comparison of the zebrafish and mouse border zone we have identified hmga1a as a key determinator of cardiac regenerative potential. Overall design: Tgnppa:mCitrine  positive cells showing high mCitrine expression were isolated from cyoinjured zebrafish hearts 7 xxx post injury. From 12 hmga1a /  mutants hearts  768 cells were isolated. From 12 hmga1a+/+ wild type hearts  768 cells were isolated. All cells were sent for single cell RNA sequencing  but one wild type plate failed during sequencing and was not used for further analysis.", null, null, null, "HUB DB 003", "GSM5017828", null, "source name:Cardiomyocytes of the Zebrafish heart ventricle|Stage:7dpi|line:Tgnppa:mCitrine;hmga1a / |tissue:Adult zebrafish ventricle", "HUB DB 003", "Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file \"cel seq2 barcodes.csv\"  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file \"cel seq2 barcodes.csv\".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: tsv files: read count matrices in which rows correspond to genes and  columns to single cells.", "Cardiomyocytes of the Zebrafish heart ventricle", "Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions. Transgenic tgnppa:mCitrine cells were subsequently FACS sorted based on mCherry expression in 384 well plates  each well containing 1 cell.", "Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016", null, "Stage:7dpi|line:Tgnppa:mCitrine;hmga1a / |tissue:Adult zebrafish ventricle", "GSM5017828", "GSM5017828: HUB DB 003; Danio rerio; RNA Seq", "GSM5017828", null, "1", "Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016", "GEO Accession:GSM5017828", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP301573", null, null, "HUB-DB-003_AHVKTGBGX7_S6_L004_R1_001.fastq.gz HUB-DB-003_AHVKTGBGX7_S6_L004_R2_001.fastq.gz", "fastq fastq", 414000732.0, 4813962.0, "GSM5017828 r4", "0:26 1:60", "A:112224009;C:76213738;G:80259829;T:145201785;N:101371", 26, 60, null, null, 112224009, 76213738, 80259829, 145201785, 101371, "SRX9841727", "SRS8023816", "SRA1183369", "GEO", "FLI", 2, 0.10103, 0.71991, 0.09307, 0.25283, 0.98932, 0.93683, 0.53111, 0.51224, 26, 60, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "trueseq", "sc", "single_cell_plate", "celseq", null, "Germany", "2021-01-13", "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": ["62890"], "units": {}, "query_ms": 8.811818996036891}