{"database": "metadata", "table": "run_metadata", "rows": [[48358, "SRR5893044", "SRX3058801", "SRS2404514", "SRP149556", "PRJNA473824", "mRNA structure dynamics identifies RNA remodelers and functional elements during embryogenesis: mRNA seq", "PRJNA473824", "Other", "RNA folding plays a crucial role in RNA function. However  our knowledge of the global structure of the transcriptome is limited to steady state conditions  hindering our understanding of how RNA structure dynamics influences gene function. Here  we have characterized mRNA structure dynamics during the maternal to zygotic transition in zebrafish. We observe that on a global level  translation guides structure rather than structure guides translation. We detect a decrease in structure in translated regions  and identify the ribosome as a major remodeler of RNA structure in vivo. In contrast  we find that three prime UTRs form highly folded structures in vivo  which can affect gene expression by modulating miRNA activity. Furthermore  we find that dynamic three prime UTR structures are enriched in RNA decay elements  including regulatory elements in nanog  and cyclin A1  key maternal factors orchestrating the maternal to zygotic transition. These results reveal a central role of RNA structure dynamics in gene regulatory programs during embryogenesis.This is the developmental mRNA seq timecourse part of the study.", null, null, null, "Developmental timecourse   WT 64c pA B1", "dev timecourse AG00644", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|molecule:RNA|selection:pA|replicate group:1|replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Developmental timecourse   WT 64c pA B1", "AG00644.1", "AG00644.1", "RNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP149556", null, null, "AG00644.1_R1.fastq.gz AG00644.1_R2.fastq.gz", "fastq fastq", 2457941384.0, 16170667.0, "AG00644.1 R2.fastq.gz", "0:76 1:76", "A:655179090;C:570607586;G:571155579;T:658430586;N:2568543", 76, 76, null, null, 655179090, 570607586, 571155579, 658430586, 2568543, "SRX3058801", "SRS2404514", "SRA596275", "Yale_Giraldez|Genetics", "Yale_Giraldez_Group", 2, 0.94406, 0.94075, 0.02483, 0.02699, 0.76936, 0.76966, 0.48505, 0.48646, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2018-06-07", "Cleavage", "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": ["48358"], "units": {}, "query_ms": 8.787354998275987}