{"database": "metadata", "table": "run_metadata", "rows": [[63406, "SRR13777260", "SRX10162830", "SRS8314486", "SRP307942", "PRJNA704625", "RNA sequencing analysis of ZsYellow negative cells and ZsYellow positive cardiopharyngeal progenitors and cardiomyocytes purified from the same 14 16 somites stage Tgnkx2.5:ZsYellow zebrafish embryos", "GSE167416", "Transcriptome Analysis", "The identification of novel cardiomyocyte intrinsic factors that support ventricular function will expand the number of candidate genes and therapeutic options for heart failure  a leading cause of death worldwide. Here  we demonstrate that a conserved RNA binding protein RBPMS2 is required for ventricular function in zebrafish and for myofibril organization and the regulation of intracellular calcium dynamics in zebrafish and human cardiomyocytes. A differential expression screen uncovered co expression of rbpms2a and rbpms2b in zebrafish cardiomyocytes. Double knockout embryos suffer from compromised ventricular filling during the relaxation phase of the cardiac cycle  which significantly reduces cardiac output. Evaluating rbpms2 null embryos with splicing sensitive differential expression analysis  quantitative PCR  and in situ hybridization revealed differential alternative splicing of cardiomyopathy genes including myosin binding protein C3 mybpc3 and phospholamban pln. Cardiomyocytes in double mutant ventricles and those derived from RBPMS2 null human induced pluripotent stem cells exhibit myofibril disarray and calcium handling abnormalities. Taken together  our data suggest that RBPMS2 performs a conserved role in regulating alternative splicing in cardiomyocytes  which is required for sarcomere organization  optimal calcium handling  and cardiac function. Overall design: Tgnkx2.5:ZsYellow zebrafish embryos at the 14 16 somites stage were dissociated to single cells and their ZsYellow positive cardiopharyngeal progenitors and cardiomyocytes were purified by fluorescence activated cell sorting. ZsYellow negative cells from the same embryos were collected in parallel. RNA sequencing analysis was performed on both populations two replicates each and differentially expressed genes were identified.", null, "pubmed:36367103", null, "ZsYellow positive cardiopharyngeal progenitors and cardiomyocytes   replicate 2", "GSM5104955", null, "source name:14 16 somites stage Tgnkx2.5:ZsYellow zebrafish embryos|strain:laboratory strain|tissue:ZsYellow positive cardiopharyngeal progenitors and cardiomyocytes|age:14 16 somites stage|genotype:Tgnkx2.5:ZsYellow", "ZsYellow positive cardiopharyngeal progenitors and cardiomyocytes   replicate 2", "Illumina Offline BaseCaller1.9.3 software used for basecalling. Quality control: Reads were aligned against Zv9/danRer7 using bwa mem v. 0.7.12 r1039 with flags \u2013t 16 \u2013f and mapping rates  fraction of multiply mapping reads  number of unique 20 mers at the 5\u2019 end of the reads  insert size distributions and fraction of ribosomal RNAs were calculated using dedicated perl scripts and bedtools v. 2.25.0.64 In addition  each resulting bam file was randomly down sampled to a million reads  which were aligned against Zv9/danRer7 and read density across genomic features were estimated for RNA Seq specific quality control metrics. Read mapping and quantification: Salmon v. 1.2.1  was used with the following flags:   quant   l IU     validateMappings in paired end mode against the GRCz11/danRer11 genome assembly and ENSEMBL 100 annotation  using all GRCz11 sequences as decoys. Quantification files were processed in R using the TxImport function and per gene counts and TPM estimates were retrieved. Genome build: Zv11/danRer11 Supplementary files format and content: Matrix table with counts and log2 TPM values for every gene and every sample", "14 16 somites stage Tgnkx2.5:ZsYellow zebrafish embryos", null, "Trizol lysis  chloroform extraction and column based purification Qiagen RNeasy Kit. RNA sample quality was evaluated using a 2100 Bioanalyzer Instrument Agilent Technologies. Approximately 50ng of RNA per sample were used to prepare sequencing libraries with the Clontech low input RNA library preparation kit. Libraries were sequenced as paired end 2x50nt on an Illumina HiSeq2500 instrument. polyA based RT priming followed by tagmentation based RNA Seq protcol", null, "strain:laboratory strain|tissue:ZsYellow positive cardiopharyngeal progenitors and cardiomyocytes|age:14 16 somites stage|genotype:Tgnkx2.5:ZsYellow", "GSM5104955", "GSM5104955: ZsYellow positive cardiopharyngeal progenitors and cardiomyocytes   replicate 2; Danio rerio; RNA Seq", "GSM5104955", null, "1", "Trizol lysis  chloroform extraction and column based purification Qiagen RNeasy Kit. RNA sample quality was evaluated using a 2100 Bioanalyzer Instrument Agilent Technologies. Approximately 50ng of RNA per sample were used to prepare sequencing libraries with the Clontech low input RNA library preparation kit. Libraries were sequenced as paired end 2x50nt on an Illumina HiSeq2500 instrument. polyA based RT priming followed by tagmentation based RNA Seq protcol", "GEO Accession:GSM5104955", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP307942", null, null, "130107Bur_D13-183_1_sequence.fastq.gz 130107Bur_D13-183_2_sequence.fastq.gz", "fastq fastq", 4545216160.0, 56815202.0, "GSM5104955 r1", "0:40 1:40", "A:1317905013;C:913569716;G:959980240;T:1351063436;N:2697755", 40, 40, null, null, 1317905013, 913569716, 959980240, 1351063436, 2697755, "SRX10162830", "SRS8314486", "SRA1199702", "GEO", "BioMicro Center / IGE, Biology / Koch Institute / Bioengineering / CEHS, Massachusetts Institute of Technology", 2, 0.93062, 0.75104, 0.14171, 0.10526, 0.74223, 0.76134, 0.49218, 0.4928, 40, 40, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2021-02-24", "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": ["63406"], "units": {}, "query_ms": 7.180756001616828}