{"database": "metadata", "table": "run_metadata", "rows": [[40165, "SRR2921972", "SRX1432515", "SRS1163510", "SRP066192", "PRJNA302179", "Genome\u2013wide transcriptional profiling with spatial resolution identifies Bone Morphogenetic Protein signaling as essential regulator of zebrafish cardiomyocyte regeneration.", "GSE74652", "Transcriptome Analysis", "In contrast to mammals  zebrafish regenerate heart injuries via proliferation of cardiomyocytes located at the wound border. Here  we show that tomo seq can be used to identify whole genome transcriptional profiles of the injury zone  the border zone and the healthy myocardium. Interestingly  the border zone is characterized by the re expression of embryonic cardiac genes that are also activated post myocardial infarction in mouse and human  including targets of Bone Morphogenetic Protein BMP signaling. Endogenous BMP signaling has been reported to be detrimental to mammalian cardiac repair. In contrast  we find that genetic or chemical inhibition of BMP signaling in zebrafish reduces cardiomyocyte dedifferentiation and proliferation  ultimately compromising myocardial regeneration  while bmp2b overexpression is sufficient to enhance it. Our results provide a resource for further studies on the molecular regulation of cardiac regeneration and reveal intriguing differential cellular responses of cardiomyocytes to a conserved signaling pathway in regenerative versus non regenerative hearts. Overall design: To generate spatially resolved RNA seq data for injured zebrafish hearts 3 and 7 xxx post injury  we cryosectioned samples  extracted RNA from the individual sections  and amplified and barcoded mRNA using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 with a few modifications. Libraries were sequenced on Illumina NextSeq  using 75bp paired end sequencing.", null, "pubmed:26748692", null, "zebrafish heart WT 3dpi #1", "GSM1924887", null, "source name:cryoinjured ventricle of the heart|tissue:adult heart|sectioning direction:injury area   uninjured  remote myocardium|sectioning thickness:12 \u00b5m|embedding strategy:extracted heart at 3 days post cryoinjury", "zebrafish heart WT 3dpi #1", "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. The right mate of each read pair was mapped to the ensemble of all transcripts and to the set of 92 ERCC spike ins in sense direction. Reads mapping equally to multiple loci were discarded. Mapped reads were assigned to sections based on barcodes according to the CEL seq protocol Hashimshony et al.  Cell Reports  2012 Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and columns to sections", "cryoinjured ventricle of the heart", "Unfixed ventricle was embedded in tissue freezing medium. Blocks were cryosectioned  and individual slices were transferred to Eppendorf tubes on dry ice. For extended experimental procedure see also Junker et al. 2014 Cell.", "RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see: Junker et al.  2014  Cell", null, "tissue:adult heart|sectioning direction:injury area   uninjured  remote myocardium|sectioning thickness:12 \u00b5m|embedding strategy:extracted heart at 3 days post cryoinjury", "GSM1924887", "GSM1924887: zebrafish heart WT 3dpi #1; Danio rerio; RNA Seq", "GSM1924887", null, "1", "RNA was isolated by TRIzol extraction. mRNA was barcoded and amplified using the CEL seq protocol Hashimshony et al.  Cell Reports  2012 see: Junker et al.  2014  Cell", "GEO Accession:GSM1924887", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP066192", null, null, "FKHEART3_R1.fastq.gz FKHEART3_R2.fastq.gz", "fastq fastq", 784558404.0, 5209213.0, "GSM1924887 r1", "0:75.22 1:75.39", "A:291009319;C:102718146;G:111606154;T:279144074;N:80711", 75, 75, null, null, 291009319, 102718146, 111606154, 279144074, 80711, "SRX1432515", "SRS1163510", "SRA311639", "GEO", "Jeroen Bakkers, Hubrecht Institute", 2, 0.12872, 0.82031, 0.12623, 0.08476, 0.99997, 0.82828, 0.0, 0.566, 76, 76, "T", "B", "mate1 technical by mapping diff", "illumina", "nextseq", "full_length", "random_priming", "unknown", "sc", "single_cell_plate", "celseq", null, "Netherlands", "2015-11-03", "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": ["40165"], "units": {}, "query_ms": 10.510395004530437}