{"database": "metadata", "table": "run_metadata", "rows": [[39761, "SRR2127900", "SRX1118698", "SRS1011435", "SRP061587", "PRJNA290964", "Next Generation Sequencing Facilitates Quantitative Analysis of Ochratoxin A treated with 6 hpf 48 hpf zebrafish embryos", "GSE71346", "Transcriptome Analysis", "To investigate the effects of ochratoxin A on microRNA expressions in zebrafish embryos. Overall design: Ochratoxin A  mediated miRNA expression in zebrafish embryos which were exposed from 6 hpf ttwo xxx hpf with doses of 0 and 0.5 micromolar.", null, "pubmed:30090366", null, "6 48 control [miRNA seq]", "GSM1832840", null, "tissue:embryo control|strain:Wild Type AB line|developemental stage:6 hpf embryos|exposed to:n1 control", "6 48 control [miRNA seq]", "Initially  the sequences generated went through a filtering process to obtain qualified reads. ConDeTri was implemented to trim or remove the reads according to the quality score. Qualified reads post filtering low quality data were analyzed using miRDeep2 to clip the 3\u2032 adapter sequence and discarding reads shorter than 18 nucleotides  before aligning reads to the  Zebrafish  genome from UCSC. Only reads that mapped perfectly to the genome five or less times were used for miRNA detection  since miRNAs usually map to few genomic locations. MiRDeep2 estimates expression levels of known miRNAs  and also identifies novel miRNAs. Genome build: GCF 000002035.4 Supplementary files format and content: bed file for the location of miRNA mapped to chromosome", "embryo control", "6 hpf embryos  were treated with ochratoxin A 0.5 mM till 48 hpf.", "Total RNA was extracted by Trizol\u00ae Reagent Invitrogen  USA according to the instruction manual. RNA purified was quantified at OD260nm by using a ND 1000 spectrophotometer Nanodrop Technology  USA and qualitated by using a Bioanalyzer 2100 Agilent Technology  USA with RNA 6000 labchip kit Agilent Technologies  USA. The small RNA library construction and deep sequencing was carried out at biotechnology company Welgene  Taipei  Taiwan. Samples were prepared using Illumina sample preparation kit according to the TruSeq Small RNA Sample Preparation Guide.The 3\u2032 and 5\u2032 adaptors were ligated to total RNA and reverse transcription followed by PCR amplification. The enriched cDNA constructs were size fractionated and purified on a 6% polyacrylamide gel electrophoresis and the bands containing the 18 40 nucleotide RNA fragments 140 155 nucleotide in length with both adapters.\u00a0 Libraries were sequenced on an Illumina GAIIx instrument 50 cycle single read . Sequencing data was processed with the Illumina software", "zebrafish embryos were selected at 6 hph with normal development.", "strain:Wild Type AB line|developemental stage:6 hpf embryos|exposed to:n1 control", "GSM1832840", "GSM1832840: 6 48 control [miRNA seq]; Danio rerio; miRNA Seq", "GSM1832840", null, "1", "Total RNA was extracted by Trizol\u00ae Reagent Invitrogen  USA according to the instruction manual. RNA purified was quantified at OD260nm by using a ND 1000 spectrophotometer Nanodrop Technology  USA and qualitated by using a Bioanalyzer 2100 Agilent Technology  USA with RNA 6000 labchip kit Agilent Technologies  USA. The small RNA library construction and deep sequencing was carried out at biotechnology company Welgene  Taipei  Taiwan. Samples were prepared using Illumina sample preparation kit according to the TruSeq Small RNA Sample Preparation Guide.The 3\u2032 and 5\u2032 adaptors were ligated to total RNA and reverse transcription followed by PCR amplification. The enriched cDNA constructs were size fractionated and purified on a 6% polyacrylamide gel electrophoresis and the bands containing the 18 40 nucleotide RNA fragments 140 155 nucleotide in length with both adapters.\u00a0 Libraries were sequenced on an Illumina GAIIx instrument 50 cycle single read . Sequencing data was processed with the Illumina software", "GEO Accession:GSM1832840", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP061587", null, null, "6_48_control.fastq.gz", "fastq", 308947811.0, 6107500.0, "GSM1832840 r1", "0:50.58 1:0", "A:75126425;C:71798677;G:85490341;T:76532368;N:0", 50, 0, null, null, 75126425, 71798677, 85490341, 76532368, 0, "SRX1118698", "SRS1011435", "SRA280185", "GEO", "ntu", 1, 0.00833, null, 0.00166, null, 0.99476, null, 0.42762, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Unknown", "2015-07-25", "Gastrula", "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": ["39761"], "units": {}, "query_ms": 7.995423999091145}