{"database": "metadata", "table": "run_metadata", "rows": [[41360, "SRR4342166", "SRX2209221", "SRS1726581", "SRP090801", "PRJNA345325", "Comparison of tbx5 positive ventricular cardiomyoctes with the rest of ventricular cardiomyocytes from adult zebrafish hearts", "GSE87596", "Transcriptome Analysis", "In vertebrates  the heart has two main layers of cardiac muscle  a peripheral compact layer and an internal trabecular layer. Little is known on the differerences in gene expression between both layers. In zebrafish the outer layer is named cortical layer and the internal also trabecular layer. Here we used a double transgenic line labelling with GFP tbx5 positive cells and cardiomyoctes with nuclear DsRed nucDsRed to distinguish cortical from trabecular myocardium. Then  we compared the transcriptome of trabecular and cortical myocardium in the adult zebrafish. We describe that Tbx5a is a good marker of trabecular myocardium. Overall design: Four paired biological replicates consisting on Tbx5 positive and Tbx5 negative adult zebrafish ventricular cardiomyocytes were analysed by RNA seq to compare their transcriptomic profiles.", null, "pubmed:29382818", null, "tbx5 2neg", "GSM2334959", null, "source name:Heart|age:Adult|tissue:Heart|cell type:Tbx5 negative ventricular cardiomyocytes|pair:2", "tbx5 2neg", "Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline. Sequencing adaptor contaminations were removed from reads using cutadapt. Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3. Genome build: Ensembl genebuild 75 Danio rerio assembly Zv9. Supplementary files format and content: matrix table.xls file contains ENSEMBL gene Ids and TMM Normalized counts per million for each sample.", "Heart", "GFP/nucDsRed and nucDsRed cells were isolated using FAC sorting from Tgtbx5:GFP/myl7:nucDsRed double transgenic adult zebrafish cardiac ventricles. Cells were sorted using SONY Synergy sy3200.", "RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions. 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification.  The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit\u00ae fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads.  4 biological replicates consisting of 5 pooled hearts were used per sample.", "All experiments were conducted with adult zebrafish between 6 month and 9 month of age  raised at a density of 3 fish/l.", "age:Adult|tissue:Heart|cell type:Tbx5 negative ventricular cardiomyocytes|pair:2", "GSM2334959", "GSM2334959: tbx5 2neg; Danio rerio; RNA Seq", "GSM2334959", null, "1", "RNA was extracted using Arcturus Pico Pure Thermofisher following manufacturer instructions. 0.6 ng of total RNA was used to generate barcoded RNA seq libraries using the Ovation Single Cell RNA Seq System NuGEN with two rounds of library amplification.  The size of the libraries was calculated using the Agilent 2100 Bioanalyzer. Library concentration was determined using the Qubit\u00ae fluorometer ThermoFisher Scientific. Libraries were sequenced on a HiSeq2500 Illumina to generate 60 bases single reads.  4 biological replicates consisting of 5 pooled hearts were used per sample.", "GEO Accession:GSM2334959", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP090801", null, null, "tbx5_2neg__HectorSanchez_RNA_Seq_OvationSC_TGGTGA_L001_R1_001.fastq.gz", "fastq", 719361654.0, 11792814.0, "GSM2334959 r1", "0:61", "A:210895656;C:137890002;G:180431743;T:190135096;N:9157", 61, null, null, null, 210895656, 137890002, 180431743, 190135096, 9157, "SRX2209221", "SRS1726581", "SRA481772", "GEO", "Bioinformatics Unit, CNIC", 1, 0.76636, null, 0.15624, null, 0.8547, null, 0.52604, null, 61, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "Spain", "2016-10-04", "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": ["41360"], "units": {}, "query_ms": 10.061680994112976}