{"database": "metadata", "table": "run_metadata", "rows": [[41246, "SRR3953259", "SRX1977495", "SRS1585136", "SRP079896", "PRJNA335352", "Next Generation Sequencing NGS of zebrafish larvae microRNA expression profilling by 2 2'' 4 4'' tetrabromodiphenyl ether BDE47 treatment", "GSE84845", "Transcriptome Analysis", "Purpose: We report the application of NGS for the impacts of BDE47 exposure on the miRNA expression profiling of zebrafish larvae. Methods: miRNA profiles of 6 dpf BDE47 treated and control zebrafish larvae were generated by deep sequencing using Illumina Hisq 2000 platform. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. Results: Compared BDE47 treatments with solvent control  a dozen of validated zebrafish miRNAs  including dre miR 142a 3p  dre miR 142b 5p  dre miR 144 3p  dre miR 146a  dre miR 190a  dre miR 219 5p  dre miR 301b 3p  dre miR 459 5p  rno miR 33 5p  dre miR 735 3p  and dre miR 735 5p  significantly changed their expressions. Conclusions: This study provides a framework for the application of high throughput sequencing towards characterization of the impacts of BDE47 on whole zebrafish larval miRNA expression profiling. Overall design: Examination of zebrafish larvae miRNA expression profilings with blank  vehicle and 2 different concentrations of BDE47 treatments.", null, "pubmed:28072866", null, "s DMSO vehicle miRNA", "GSM2252182", null, "source name:6 dpf larvae|strain:Tuebingen|tissue:whole larvae|age:6 dpf", "s DMSO vehicle miRNA", "Illumina Casava1.7 software used for basecalling. post obtained from the raw sequencing data  clean reads were mapped into reference zebrafish genome Zv10 assembly. Trimmed mean of M values of library size TMM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. Genome build: zv10 Supplementary files format and content: tab delimited text files include TMM values for each Sample.", "6 dpf larvae", null, "Zebrafish larvae were homogenized  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 \u03bcg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.", null, "strain:Tuebingen|tissue:whole larvae|age:6 dpf", "GSM2252182", "GSM2252182: s DMSO vehicle miRNA; Danio rerio; miRNA Seq", "GSM2252182", null, "1", "Zebrafish larvae were homogenized  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 \u03bcg of total RNA for the construction of sequencing libraries. miRNA libraries were prepared for sequencing using standard Illumina protocols.", "GEO Accession:GSM2252182", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP079896", null, null, "Sample_s_1_filtered.fq.gz", "fastq", 383701320.0, 16988819.0, "GSM2252182 r1", "0:22.59 1:0", "A:97700155;C:85144858;G:93319367;T:107531046;N:5894", 22, 0, null, null, 97700155, 85144858, 93319367, 107531046, 5894, "SRX1977495", "SRS1585136", "SRA444471", "GEO", "Tongji University", 1, 0.86023, null, 0.05501, null, 0.89534, null, 0.59715, null, 22, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "China", "2016-07-26", "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": ["41246"], "units": {}, "query_ms": 9.438229000807041}