{"database": "metadata", "table": "run_metadata", "rows": [[36735, "SRR836195", "SRX272884", "SRS417390", "SRP021915", "PRJNA200706", "Ribosome Profiling over a Zebrafish Developmental Timecourse", "GSE46512", "Transcriptome Analysis", "To experimentally validate the non coding status of annotated lncRNAs  we performed ribosome profiling over a developmental timecourse that matched our previously published Pauli et al. 2012 developmental transcriptome. We find that many previously annotated lncRNAs appear to be translated  but in a pattern more akin to five prime' leaders of coding genes. Overall design: Ribosome profiling over 8 stages in early zebrafish development: 2 4 cell  256 cell  1K cell  Dome  Shield  Bud  28hpf and 5dpf", null, "pubmed:23698349", null, "20120724 RPF Seq Dome", "GSM1131533", null, "tissue:Whole embryos|developmental stage:Dome|strain:TL/AB|target molecule:ribosome footprinted RNA", "20120724 RPF Seq Dome", "Adapters trimmed using custom script Reads that mapped to zebrafish rRNAs SILVA rRNA database: http://www.arb silva.de/ by Bowtie2  N 1  L 20  k 20 were discarded Remaining reads mapped to previously assembled zebrafish developmental transcriptome Pauli et al. 2012 on top of the Zv9/danRer7 assembly of the zebrafish genome by Tophat2; no indels  no novel junctions   M  g 10 Only RPFs of length 27nt to 32nt used. P site positions determined to be +12 for 27 28nt RPFs  +13 for 29 31nt RPFs  +13 for 29 31nt RPFs  +14 for 32nt RPFs. Custom scripts used to generate bw files of genome wide ribosome profiles corresponding to P site occupancy  in conjunction with BedTools and UCSC bedgraphToBedBed Genome build: Zv9 danRer7 Supplementary files format and content: bigwig files corresponding to P site occupancy by ribosomes", "Whole embryos", "Embryos were quickly washed in ice cold PBS and flash frozen in liquid nitrogen", "Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4  250 mM NaCl  15 mM MgCl2  1mM dithiothreitol  100 \u03bcg/ml cycloheximide with added 0.5% Triton X 100  500 \u03bcg/ml GMP PNP  24 U/ml TurboDNase Ambion AM2238  incubated with agitation for 10 min at 4\u00b0C  and clarified by centrifugation at 1300 rcf for 10 min at 4\u00b0C. 20\u03bcl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37\u00b0C  then stopped by chilling on ice and addition of 40 \u03bcl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4\u00b0C  and resuspended in 800 \u03bcl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011", "400 600 embryos per stage from TL/AB WT strains were allowed to grow at 28.5\u00b0C and staged according to Kimmel et al. Dev. Dyn. 1995", "developmental stage:Dome|strain:TL/AB|target molecule:ribosome footprinted RNA", "GSM1131533", "GSM1131533: 20120724 RPF Seq Dome; Danio rerio; RNA Seq", "GSM1131533 1", null, "1", "Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4  250 mM NaCl  15 mM MgCl2  1mM dithiothreitol  100 \u03bcg/ml cycloheximide with added 0.5% Triton X 100  500 \u03bcg/ml GMP PNP  24 U/ml TurboDNase Ambion AM2238  incubated with agitation for 10 min at 4\u00b0C  and clarified by centrifugation at 1300 rcf for 10 min at 4\u00b0C. 20\u03bcl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37\u00b0C  then stopped by chilling on ice and addition of 40 \u03bcl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4\u00b0C  and resuspended in 800 \u03bcl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011", "GEO Accession:GSM1131533", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP021915", null, null, "20120724_RPF-Seq_Dome.fastq.gz", "fastq", 5455941832.0, 123998678.0, "GSM1131533 r1", "0:44", "A:1174530251;C:1596486361;G:1605087499;T:1077423125;N:2414596", 44, null, null, null, 1174530251, 1596486361, 1605087499, 1077423125, 2414596, "SRX272884", "SRS417390", "SRA075002", "GEO", "Schier, Dept of Molecular and Cellular Biology, Harvard University", 1, 0.00739, null, 0.0007, null, 0.99898, null, 0.86907, null, 44, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "5prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-04-30", "Blastula", "Embryo", "Whole Organism", "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": ["36735"], "units": {}, "query_ms": 8.263312993221916}