{"database": "metadata", "table": "run_metadata", "rows": [[29569, "SRR27368685", "SRX23045203", "SRS20006222", "SRP480346", "PRJNA1057908", "An in vivo repertoire of zebrafish cardiomyocyte specific cis regulatory elements [RNA Seq]", "GSE252151", "Transcriptome Analysis", "cis Regulatory elements cREs are essential for the spatio temporal control of gene expression during development and disease. However  cRE activity is highly dependent on cell and tissue type. The developing heart is composed of several cell types  predominantly cardiomyocytes. Therefore  cardiomyocytes specific modelling is required to understand the cis regulation of the developing heart. Zebrafish are an ideal model to study heart development  as they share a number of physiological features with the human heart during development. Therefore  we present a comprehensive cardiomyocyte specific repertoire of cREs isolated from zebrafish larvae. This data combines live transcriptomics and epigenetic profiling  providing insights into cREs and their associated genes involved in heart development. We further perform a transgenic reporter assay for the identified cREs of bmp10 and popdc2 genes  validating these genomic regions as cardiac regulatory elements. We share this comprehensive  reproducible cardiomyocyte specific cRE resource as an interrogable web tool for understanding the epigenetic and transcriptomic mechanisms underlying heart development and emergence of congenital heart defects. Overall design: Cardiomyocytes were isolated from the Tgmyl7::GFP zebrafish transgenic line. Larvae were collected 72 hpf GFP positive 30 000 cells  n=3 biological replicates and GFP negative cells 500 000 cells  n=3 biological replicates were collected  and RNA sequencing was performed on these samples.", "parent bioproject:PRJNA1057890", null, null, "500kGFPneg6 Non cardiomyocytes", "GSM7995233", null, "source name:Heart|tissue:Heart|cell line:Primary cells|cell type:Non cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPneg|treatment:Control|geo loc name:missing|collection date:missing", "500kGFPneg6 Non cardiomyocytes", "FASTQ files were quality trimmed for overrepresented sequences using Cutadapt version 1.16 Martin  2011. The files were then processed for mapping and obtaining read counts with RNAsik Tsyganov et al  2018  using default parameters. There were two sets of counts obtained  the first were the reads mapped to genome Zv9  and the second to genome Zv10. Read counts obtained from mapping to Zv10 were used for RNA seq analysis and visualizations. Read counts obtained from mapping to Zv9 were used for RNA seq analysis to obtain a set of DEGs and were then used to overlap with the genes associated to peaks of the ChIP seq data sets. Assembly: Zv9  Zv10 Supplementary files format and content: txt.gz: compressed tab delimited text files include count values for each sample", "Heart", null, "RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866  Qubit\u2122 RNA HS Assay Kit Q32852  ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Heart|cell line:Primary cells|cell type:Non cardiomyocytes|genotype:Tgmyl7::GFP|gfp status:GFPneg|treatment:Control", "GSM7995233", "GSM7995233: 500kGFPneg6 Non cardiomyocytes; Danio rerio; RNA Seq", "GSM7995233 r1", "GSM7995233", "1", "RNA extraction was performed using the RNEasy Plus Micro Kit Qiagen according to the instructions provided in the manual. Integrity of the extracted RNA was assessed with BioAnalyzer Agilent and the concentration was measured with Qubit Q32866  Qubit\u2122 RNA HS Assay Kit Q32852  ThermoFisher Scientific. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP480346", null, null, "500kGFPneg6_S42_L008_R1_001.fastq.gz", "fastq", 527477356.0, 10449387.0, "GSM7995233 r1", "0:50.48", "A:141759410;C:113279303;G:116384028;T:155860577;N:194038", 50, null, null, null, 141759410, 113279303, 116384028, 155860577, 194038, "SRX23045203", "SRS20006222", "SRA1776396", "Australian Regenerative Medicine Institute, Monash University", "Australian Regenerative Medicine Institute, Monash University", 1, 0.79175, null, 0.2711, null, 0.7587, null, 0.61924, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Australia", "2023-12-27", "Undetermined", "Larval", "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": ["29569"], "units": {}, "query_ms": 11.133325002447236}