{"database": "metadata", "table": "run_metadata", "rows": [[69600, "SRR18927204", "SRX15004839", "SRS12753551", "SRP372368", "PRJNA832312", "Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2", "GSE201611", "Transcriptome Analysis", "The endocardium plays important roles in the development and function of the vertebrate heart; however  few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here  we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity  we employed npas4l  etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants  significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression  whereas Bmp inhibition decreased expression. Finally  epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast  overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together  these results describe the differentiation of the endocardium  distinct from vasculature  and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish  three independent biological replicates were collected for each condition", null, "pubmed:35531980", null, "FAC sorted GFP cells  15 s Gtendocard:egfp  rep 1", "GSM6068599", null, "source name:Endocardium|tissue:Endocardium|transgenic line:GtSAGFF27C; Tg4xUAS:egfp|genotype:WT|developmental stage:15 somite stage", "FAC sorted GFP cells  15 s Gtendocard:egfp  rep 1", "Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output", "Endocardium", null, "Embryos were collected  deyolked  and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries  libraries were prepared using the Smart seq2 protocol as described by Picelli et al.  2014 PMID:24385147", "Fish were allowed to lay eggs in a 30 minute window  fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23\u2103 overnight then allowed to grow at 28.5\u2103 until they reached the 15 somite stage", "tissue:Endocardium|transgenic line:GtSAGFF27C; Tg4xUAS:egfp|genotype:WT|developmental stage:15 somite stage", "GSM6068599", "GSM6068599: FAC sorted GFP cells  15 s Gtendocard:egfp  rep 1; Danio rerio; RNA Seq", "GSM6068599 r1", "GSM6068599", "1", "Embryos were collected  deyolked  and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries  libraries were prepared using the Smart seq2 protocol as described by Picelli et al.  2014 PMID:24385147", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP372368", null, null, "endocardegfp_01_S1_L001_R1_001.fastq.gz", "fastq", 738191052.0, 10120241.0, "GSM6068599 r1", "0:72.94 1:0", "A:201379342;C:167003879;G:171545653;T:197622863;N:639315", 72, 0, null, null, 201379342, 167003879, 171545653, 197622863, 639315, "SRX15004839", "SRS12753551", "SRA1410588", "Department of Anatomy & Physiology, The University of Melbourne", "Department of Anatomy & Physiology, The University of Melbourne", 1, 0.94529, null, 0.0782, null, 0.74485, null, 0.47776, null, 75, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "Australia", "2022-04-26", "Segmentation", "Embryo", "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": ["69600"], "units": {}, "query_ms": 12.837418995331973}