{"database": "metadata", "table": "run_metadata", "rows": [[38326, "SRR1732702", "SRX821998", "SRS801693", "SRP051503", "PRJNA271079", "Discovering miRNA regulatory networks in Holt Oram Syndrome using a Zebrafish model [miRNA seq]", "GSE64465", "Transcriptome Analysis", "To investigate the complex regulatory networks disrupted in Holt Oram Syndrome  we characterized genome widely the miRNA and mRNA expression profiles in WT and Tbx5 depleted zebrafish embryos at two development time points  24 hpf and 48 hpf. Overall design: The zebrafish gene Tbx5a was silenced with antisense morpholino oligonucleotide MO Tbx5a against the TSS of the gene. A MO CT was used in CT samples. 1 5ng morpholinos were injected into the yolk of 1 cell stage embryos and total RNA extracted from xxx embryos collected at xxx and 48hpf.The Zebrafish  wild type AB strain line was used.", "parent bioproject:PRJNA271069", "pubmed:27471727", null, "Emb MO Tbx5a 24hpf rep1", "GSM1571855", null, "source name:Embryos  MO Tbx5a  24hpf  replicate1|tissue:embryo|strain:AB|treatment:Mo MOTbx5a injection|developmental stage:24hpf", "Emb MO Tbx5a 24hpf rep1", "Basecalls performed using CASAVA v1.8 Sequenced reads were trimmed for adaptor sequence. Reads were algned to miRBase v20 using miRExpress v2.1.3 Normalized abundance measurements from DESeq Genome build: miRBase v20 Supplementary files format and content: tab delimited text file includes normalized read count per sample", "Embryos  MO Tbx5a  24hpf  replicate1", "1 cell stage zebrafish embryos were microinjected with 1 5 ng of morpholino against dre Tbx5a MO Tbx5a or with 1 5 ng of control morpholino", "For each library 1 \u03bcg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc.  San Diego  USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 \u00b5l elution buffer Illumina for at least 2 hours at room temperature  to enrich for molecules containing inserts in the range of 18\u201333 nt.", "Zebrafish was raised and maintained under standard laboratory conditions Westerfileld M zebrafish book in Zebrafish Housing Systems Tecniplast  Varese  Italy.", "tissue:embryo|strain:AB|treatment:Mo MOTbx5a injection|developmental stage:24hpf", "GSM1571855", "GSM1571855: Emb MO Tbx5a 24hpf rep1; Danio rerio; miRNA Seq", "GSM1571855", null, "1", "For each library 1 \u03bcg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc.  San Diego  USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 \u00b5l elution buffer Illumina for at least 2 hours at room temperature  to enrich for molecules containing inserts in the range of 18\u201333 nt.", "GEO Accession:GSM1571855", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP051503", null, null, "E.T.fq.gz", "fastq", 399134579.0, 13766109.0, "GSM1571855 r1", "0:28.99 1:0", "A:88725326;C:102855219;G:121123717;T:86418155;N:12162", 28, 0, null, null, 88725326, 102855219, 121123717, 86418155, 12162, "SRX821998", "SRS801693", "SRA221043", "GEO", "IIT, CNR", 1, 0.66472, null, 0.25948, null, 0.89623, null, 0.54913, null, 34, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Italy", "2014-12-23", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"]], "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": ["38326"], "units": {}, "query_ms": 11.482063004223164}