{"database": "metadata", "table": "run_metadata", "rows": [[37252, "SRR1039866", "SRX384676", "SRS508876", "SRP033369", "PRJNA230112", "PolyA tail profiling reveals an embryonic switch in translational control", "GSE52809", "Other", "PolyA tails enhance the stability and translation of most eukaryotic messenger RNAs  but difficulties in globally measuring polyA tail lengths have impeded greater understanding of polyA tail function. Here we describe polyA tail length profiling by sequencing PAL seq and apply it to measure tail lengths of millions of individual RNAs isolated from yeasts  cell lines  Arabidopsis thaliana leaves  mouse liver  and zebrafish and frog embryos. PolyA tail lengths were conserved between orthologous mRNAs  with mRNAs encoding ribosomal proteins and other 'housekeeping' proteins tending to have shorter tails. As expected  tail lengths were coupled to translational efficiencies in early zebrafish and frog embryos. However  this strong coupling diminished at gastrulation and was absent in non embryonic samples  indicating a rapid developmental switch in the nature of translational control. This switch complements an earlier switch to zygotic transcriptional control and explains why the predominant effect of microRNA mediated deadenylation concurrently shifts from translational repression to mRNA destabilization. Overall design: 64 samples from a variety of species", null, "pubmed:24476825", null, "Dre 155 2hpf RNA", "GSM1276547", null, "tissue:zebrafish embryo|strain:AB|developmental stage:2 hpf", "Dre 155 2hpf RNA", "Raw read files were stripped of adaptor and mapped to the appropriate species' genome and/or transcriptome. RNA seq and ribosome profiling reads mapping within the coding sequence of an annotated gene  excluding the first 50 nucleotides of the coding sequence  were assigned to that gene and used to calculate its RPKM value. PolyA tail length measurements were generated using PAL seq tags that mapped within the three prime UTR of an annotated gene. Genome build: Human: hg18; Mouse: mm9; Zebrafish: danRer7; Drosophila: dm3; Arabidopsis: tair10; S. cerevisiae: sacCer3; S. pombe: Spombe1; Xenopus: Unigene Supplementary files format and content: One set of processed data files contains abundance and polyA tail length measurements for each gene. Another set contains raw fluorescence intensities for each base for each cycle of sequencing by synthesis and streptavidin flow in for each sequencing cluster. Another set contains normalized streptavidin fluorescence intensities for each sequencing cluster.", "zebrafish embryo", "RNA seq: Cytoplasmically enriched RNA was extracted  polyA selected  randomly fragmented by partial alkaline hydrolysis and then size selected RNA fragments were used for library preparation. Ribosome profiling: Cell extracts were processed as described in Subtelny et al.  2014 GSE52809.                                 PAL seq: Polyadenylated ends in total RNA were ligated to a biotinylated adaptor  then partially digested with RNase T1. The resulting fragments were size selected 104 750 nt  captured on streptavidin beads  and used for library preparation.", "Libraries were constructed exactly as described in Subtelny et al.  2014 GSE52809", "Each sample was grown or maintained in accordance with standard protocols.", "strain:AB|developmental stage:2 hpf", "GSM1276547", "GSM1276547: Dre 155 2hpf RNA; Danio rerio; RNA Seq", "GSM1276547", null, "1", "Libraries were constructed exactly as described in Guo et al.  2010 GSE22004 RNA seq", "GEO Accession:GSM1276547", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP033369", null, null, "Dre_155_2hpf_RNA_TTAGGC-s_2_1_sequence.txt", "fastq", 1243480640.0, 31087016.0, "GSM1276547 r1", "0:40", "A:325925243;C:289644106;G:350484223;T:277122127;N:304941", 40, null, null, null, 325925243, 289644106, 350484223, 277122127, 304941, "SRX384676", "SRS508876", "SRA114402", "GEO", "Bartel, Biology, Whitehead Institute for Biomedical Research", 1, 0.10159, null, 0.02157, null, 0.94219, null, 0.88654, null, 40, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-11-27", "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": ["37252"], "units": {}, "query_ms": 13.212557008955628}