{"database": "metadata", "table": "run_metadata", "rows": [[36282, "SRR352483", "SRX100935", "SRS266974", "SRP008845", "PRJNA146609", "Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution", "GSE32880", "Other", "Thousands of large intervening non coding RNAs lincRNAs have been identified in mammals. To better understand the evolution and functions of these enigmatic RNAs  we used chromatin marks  polyA site mapping and RNA Seq data  to identify more than 550 distinct lincRNAs in zebrafish. Although these shared many characteristics with mammalian lincRNAs  only 29 had detectable sequence similarity with putative mammalian orthologs  typically restricted to a single short region of high conservation. Other lincRNAs had conserved genomic locations without xxx sequence conservation. Antisense reagents targeting conserved regions of two zebrafish lincRNAs caused developmental defects. Reagents targeting splice sites caused the same defects and were rescued by adding either the mature lincRNA or its human or mouse ortholog. Our study provides a roadmap for identification and analysis of lincRNAs in model organisms and shows that lincRNAs play crucial biological roles during embryonic development with functionality conserved despite limited sequence conservation. Overall design: H3K4me3  H3K36me3 chromatin maps  3P Seq and RNA Seq were used to identify lincRNAs in the zebrafish genome", null, "pubmed:22196729", null, "Strand specific RNA Seq 72 hpf", "GSM813761", null, "tissue:whole embryo at 72 hpf embryo|developmental stage:72 hpf", "Strand specific RNA Seq 72 hpf", "Reads were aligned to the zebrafish danRer7 genome assembly using Bowtie  allowing for up to one mismatch and up to 4 genomic matches.", "whole embryo at 72 hpf", "Anesthetized 24 hpf and 72 hpf decorioneted embryos were washed three times in PBS 137 mM NaCl  2.7 mM KCl  1.5 mM KH2PO4  8 mM Na2HP04  pH 7.4 and suspended in PBS containing 1% freshly added formaldehyde. Embryos were transferred to a dounce homogenizer  dounced several times and incubated at room temperature for 15 min. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed  and pellets were rinsed twice with PBS  flash frozen in liquid nitrogen and stored at \u201380C.", "polyA selected RNA was amplified using RiboAmp Plus RNA Amplification kit  randomly fragmented by partial alkaline hydrolysis. Size selected RNA fragments 25 45 nt were used for library preparation. Libraries were prepared as in Guo et al  2010 GSE21992", "Zebrafish embryos or adults grown under standard condition", "tissue:whole embryo|developmental stage:72 hpf", "GSM813761", "GSM813761: Strand specific RNA Seq 72 hpf", "GSM813761: Strand specific RNA Seq 72 hpf", "GSM813761: Strand specific RNA Seq 72 hpf", "1", null, "GEO Accession:GSM813761", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP008845", null, "read name barcode proc directive:ignore", "RNA_Seq_72hpf.2.fastq", "fastq", 924879168.0, 25691088.0, "GSM813761 2", "0:36", "A:218871678;C:217000200;G:266487098;T:214411336;N:8108856", 36, null, null, null, 218871678, 217000200, 266487098, 214411336, 8108856, "SRX100935", "SRS266974", "SRA047033", "GEO", "Whitehead Institute for Biomedical Research", 1, 0.47296, null, 0.10988, null, 0.86397, null, 0.59423, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2011-10-11", "Larval", "Larval", "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": ["36282"], "units": {}, "query_ms": 11.826764000034018}