{"database": "metadata", "table": "run_metadata", "rows": [[41391, "SRR4375176", "SRX2226710", "SRS1732686", "SRP090954", "PRJNA345638", "RESA identifies mRNA regulatory sequences with high resolution", "PRJNA345638", "Other", "Gene expression is regulated extensively at the level of mRNA stability  localization  and translation. However  decoding functional RNA regulatory features remains a limitation to understanding post transcriptional regulation in vivo. Here  we developed RNA Element Selection Assay RESA  a method that selects RNA elements based on their activity in vivo and uses high throughput sequencing to provide quantitative measurement of their regulatory function with near nucleotide resolution. We implemented RESA to identify sequence elements modulating mRNA stability during zebrafish embryogenesis. RESA provides a sensitive and quantitative measure of microRNA activity in vivo and also identifies novel regulatory sequences. To uncover specific sequence requirements within regulatory elements  we developed a bisulfite mediated nucleotide conversion strategy for large scale mutational analysis RESA bisulfite. Finally  we used the versatile RESA platform to map candidate protein RNA interactions in vivo RESA CLIP. The RESA platform can be broadly applicable to uncover the regulatory features shaping gene expression and cellular function.", null, null, null, "RESA Seq   WT 64c pA r3 B2", "resa AG01061", null, "strain:TU/AB|age:2.0|dev stage:64c|sex:pooled male and female|tissue:embryo|treatment:500utr|molecule:RNA|selection:pA|replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RESA Seq   WT 64c pA r3 B2", "AG01061.1", "AG01061.1", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "unspecified", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP090954", null, null, "AG01061.1_R1.fastq.gz AG01061.1_R2.fastq.gz", "fastq fastq", 724448416.0, 4766108.0, "AG01061.1 R2.fastq.gz", "0:76 1:76", "A:224701149;C:138989041;G:139762199;T:220977796;N:18231", 76, 76, null, null, 224701149, 138989041, 139762199, 220977796, 18231, "SRX2226710", "SRS1732686", "SRA482696", "Yale University|Genetics", "Yale University", 2, 0.84913, 0.84756, 0.03557, 0.03568, 0.97153, 0.97116, 0.47281, 0.46157, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-10-06", "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": ["41391"], "units": {}, "query_ms": 7.533044001320377}