{"database": "metadata", "table": "run_metadata", "rows": [[36643, "SRR700537", "SRX233123", "SRS393097", "SRP018538", "PRJNA189226", "Comparison of cardiomyocyte transcripts post knockdown of Gata4 in zebrafish embryos", "GSE44233", "Transcriptome Analysis", "The Gata4 transcription factor is essential for normal heart development  but the molecular basis for its function remain poorly understood.  We profiled at the whole genome level transcript changes in cardiomyocytes when Gata4 is depleted from zebrafish embryos.  Our objective was to elucidate the cardiomyocyte specific molecular program functioning downstream of Gata4 in order to better understand the role of Gata4 in cardiac morphogenesis. Overall design: Six samples in total are deposited.  Three replicate control samples and three replicate Gata4 morphant samples were analyzed.", null, "pubmed:23850773", null, "Seq11", "GSM1081111", null, "tissue:sorted cardiomyocytes|developmental stage:24hpf|transgenic line:tgmyl7::gfp|experimental group:Gata4 morphant", "Seq11", "Basecalls  demultiplexing  and filtering of reads was  performed using Casava 1.7.0. Read alignment was performed with the BWA alignment algorithm with native goby support using gobyweb  version: development 20110921150240 with the following parameters: Ambiguity threshold = 1  Max Number Gap Opens = 1  Max Number Gap Extensions =  1. Differential expression was generated with the DESEQ package with native goby support using gobyweb  version: development 20110921150240 with the following parameters: q value threshold = 1.0  weight adjustment = none  Gene counts box checked. Data were filtered according to geneID's demonstrating a p adjusted < 0.1  a log2 fold change > 1 for WT/G4  and Average RPKM in the comparison group > 1. Genome build: Zv9.61 Supplementary files format and content: Wig files were generated using gobyweb  version: development20110921150240.  Additional supplementary .xlsx file containing RPKM  counts  and statistical values was exported from gobyweb and processed in excel.", "sorted cardiomyocytes", "Embryos were injected with morpholino before the 4 cell stage of development.  2nl of a 0.7mM concentration of Gata4 morpholino five prime TCCACAGGTGAGCGATTATTGCTTC three prime were injected per individual embryo.  At 24 hpf  batches of approximately 200 embryos were pooled into 1.5 ml tube.  Embryos were dissociated by manual agitation with a pellet pestle Fisher and trypsinized with pre heated TrypLE Life Technologies at 32C for 15 min on a rotator. Trypsinized samples were pipetted through a 35um cell strainer into a 5ml tube  trypsin inhibited by addition of 4ml FACS buffer L 15 medium supplemented with 1% heat inactivated FCS  0.8mM CaCl2  50U/ml penicillin  and 0.05 mg/ml streptomycin followed by addition of FCS to 7.5% final concentration. Cells were pelleted at 300 RCF for 5 min and then washed with FACS buffer. Dissociated embryonic cells were resuspended at 7.5x106 cells/ml in FACS buffer. FACS was performed on a Vantage cell sorter BD into Trizol LS Life Technologies  and stored at  80C until RNA isolation.", "RNA was isolated by Trizol except that post addition of 1.5 volumes of 100% ethanol to the aqueous phase  the solution was transferred to an RNeasy minElute column Qiagen.  On column DNase digestion  subsequent washing  and RNA elution was performed according to the Qiagen's recommended protocol for RNeasy micro kit. 100ng of total RNA was used to prepare the libraries.  Libraries were prepared for RNA sequencing using the mRNA Seq seq1  seq5  and seq11 or TruSeq Kit seq13  seq14  and seq15 according to the Illumina's recommended protocol.", "Embryos were grown in 1x E3 buffer for 24 hours at 28.5 degrees Celsius in petri dishes.  25 ml of E3 buffer was used per 50 60 embryos in each dish.", "developmental stage:24hpf|transgenic line:tgmyl7::gfp|experimental group:Gata4 morphant", "GSM1081111", "GSM1081111: Seq11; Danio rerio; RNA Seq", "GSM1081111 1", null, "1", null, "GEO Accession:GSM1081111", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", null, "SRP018538", null, null, null, null, 1364181264.0, 37893924.0, "GSM1081111 r1", "0:36", "A:362442341;C:297159061;G:406723961;T:297355968;N:499933", 36, null, null, null, 362442341, 297159061, 406723961, 297355968, 499933, "SRX233123", "SRS393097", "SRA066447", "GEO", "Todd Evans Lab, Cell and Developmental Biology, Weill Cornell", 1, 0.67174, null, 0.07612, null, 0.74416, null, 0.48016, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "full_length", "random_priming", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2013-02-11", "Pharyngula", "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": ["36643"], "units": {}, "query_ms": 8.607843999925535}