{"database": "metadata", "table": "run_metadata", "rows": [[41251, "SRR3987431", "SRX1989728", "SRS1593550", "SRP080353", "PRJNA335856", "High throughput sequencing analysis identify miRNAs in 7dpf F1 zebrafish under \u00df diketone antibiotics exposure to F0 zebrafish", "GSE85004", "Transcriptome Analysis", "Small RNA high throughput sequencing technology was used to characterize the miRNAs in F1 zebrafish post 90 day \u00df diketone\u00a0antibiotic DKA exposure to F0 zebrafish at 6.25 and 12.5 mg/L. The small RNA libraries from 7 dpf F1 zebrafish were constructed. In total  10 117 347  9 818 830 and 12 049 949 raw reads were acquired  respectively  under the different DKA exposure treatments 0  6.25 mg/L and 12.5mg/L from the three miRNAs libraries by Illumina sequencing. Low quality reads were removed  which included five prime' contaminants  those missing the three prime' primer or insert tag  sequences with a poly A tail  and those shorter than 17 nt and longer than 25 nt. As a result  8 141 146 representing 312 735 unique sequences; control  8 687 210 representing 251 508 unique sequences; 6.25 mg/L  and 10 569 566 representing 441 938 unique sequences; 12.5 mg/L valid reads in the 17 to 25 nt size range were isolated for further analysis. The sRNAs from the three libraries were similar  and the unique sRNA reads were mainly distributed in the 20 24 nt range  among which 22 and 23 nt accounted for 41.8% and 20.0% of total unique sRNA reads  respectively. The 22 nt sRNAs were the most abundant  with the length distribution of counts of sequ seqs and unique miRNAs displaying a normal distribution. Overall design: Sample 1: Examination of small RNA in 7 dpf F1 zebrafish post 90 day DKA exposure to F0 zebrafish at 0 mg/L; Sample 2: Examination of small RNA in 7 dpf F1 zebrafish post 90 day DKA exposure to F0 zebrafish at 6.25 mg/L; Sample 3: Examination of small RNA in 7 dpf F1 zebrafish post 90 day DKA exposure to F0 zebrafish at 12.5 mg/L.", null, null, null, "S6 F1", "GSM2255738", null, "source name:F1 zebrafish  7 dpf  F0 6.25 mg/L DKA exposure|strain/background:AB|genotype/variation:WT|f0 treatment:6.25 mg/L DKA exposure for 90 days|tissue:F1 whole body|f1 developmental stage:7 dpf", "S6 F1", "Briefly  the raw reads were subjected to the Illumina pipeline filter Solexa 0.3  and then the dataset was further processed with an in house program  ACGT101 miR LC Sciences  Houston  Texas  USA  to remove adapter dimers  junk  low complexity  common RNA families rRNA  tRNA  snRNA  snoRNA and repeats. Subsequently  unique sequences with length in 1826 nucleotide were mapped to specific species precursors in miRBase 20.0 by BLAST search to identify known miRNAs and novel 3p  and 5p derived miRNAs. Length variation at both 3\u2019 and 5\u2019 ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA containing arm were considered to be novel 5p  or 3p derived miRNA candidates. The remaining sequences were mapped to other selected species precursors with the exclusion of specific species in miRBase 20.0 by BLAST search  and the mapped pre miRNAs were further BLASTed against the specific species genomes to determine their genomic locations. The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the specific genomes  and the hairpin RNA structures containing sequences were predicated from the flank 80 nt sequences using RNAfold software http://rna.tbi.univie.ac.at/cgi bin/RNAfold.cgi. The criteria for secondary structure prediction were: 1 number of nucleotides in one bulge in stem <=12; 2 number of base pairs in the stem region of the predicted hairpin >=16; 3 cutoff of free energy kCal/mol <=15; 4 length of hairpin up and down stems + terminal loop >=50; 5 length of hairpin loop <=20; 6 number of nucleotides in one bulge in mature region <=8; 7 number of biased errors in one bulge in mature region<=4; 8 number of biased bulges in mature region <=2; 9 number of errors in mature region <=7; 10 number of base pairs in the mature region of the predicted hairpin >=12; and 11 percent of mature in stem >=80. For normalized abundance measurements  a modified global normalization is used to correct copy numbers among different samples. Basic assumptions and procedures involved in this method are: 1. There is a subset of sequences of a significant number that do not change significantly across all samples. 2. In sequencing measurements  experimental condition variations may lead to copy number reading variations. However  in each sample run  the reading variations occur in the same proportion to all sequences. This assumption permits the use of a single correction factor for all sequences in a sample. Genome build: Zv9 ftp://ftp.ensembl.org/pub/release 66/fasta/danio rerio/dna/ Supplementary files format and content: Table8.2 S12 F1vsS6 F1vsCON F1.xlsx indicates the differential expression between two DKA exposure treatments 6.25 and 12.5 mg/L treatments and control. Supplementary files format and content: Table8.6 S12 F1vsS6 F1.xlsx indicates the differential expression between 6.25 mg/L and 12.5 mg/L DKA exposure treatments. Supplementary files format and content: Table8.7 S6 F1vsCON F1.xlsx indicates the differential expression between 6.25 mg/L DKA exposure treatment and control. Supplementary files format and content: Table8.8 S12 F1vsCON F1.xlsx indicates the differential expression between 12.5 mg/L DKA exposure treatment and control.", "F1 zebrafish  7 dpf  F0 6.25 mg/L DKA exposure", "Adult wild type zebrafish AB strain were purchased from a local supplier. Embryos at 6 hpf were exposed to control and two DKA treatments 6.25 and 12.5 mg/L composed of a mix of the six DKA species listed below with equal weight concentrations and equal volumes of each DKA species. post 90 days of DKA exposure  F1 zebrafish at 7 dpf for each group control and two DKA exposure treatments were collected. Certified DKA reference standards were sourced from Amresco Solon  OH  USA and used as received: ofluoxacin CAS No. 82419 36 1  purity of 99%  ciprofloxacin 85721 33 1  99%  enrofloxacin 93106 60 6  99%  doxycycline 24390 14 5  99%  chlortetracycline 64 72 2  95% and oxytetracycline 79 57 2  99%.", "Total RNA was extracted using Trizol reagent Invitrogen  CA  USA following the manufacturer\u2019s procedure. The total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit Agilent  CA  USA with RIN number >7.0. Approximately 1 \u03bcg of total RNA was used to prepare small RNA library according to protocol of TruSeq Small RNA Sample Prep Kits Illumina  San Diego  USA. Then  we performed the single end sequencing 36 bp on an Illumina HiSeq 2500 at the LC BIO Hangzhou  China following the vendor\u2019s recommended protocol.", null, "strain/background:AB|genotype/variation:WT|f0 treatment:6.25 mg/L DKA exposure for 90 days|tissue:F1 whole body|f1 developmental stage:7 dpf", "GSM2255738", "GSM2255738: S6 F1; Danio rerio; ncRNA Seq", "GSM2255738", null, "1", "Total RNA was extracted using Trizol reagent Invitrogen  CA  USA following the manufacturer\u2019s procedure. The total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit Agilent  CA  USA with RIN number >7.0. Approximately 1 \u03bcg of total RNA was used to prepare small RNA library according to protocol of TruSeq Small RNA Sample Prep Kits Illumina  San Diego  USA. Then  we performed the single end sequencing 36 bp on an Illumina HiSeq 2500 at the LC BIO Hangzhou  China following the vendor\u2019s recommended protocol.", "GEO Accession:GSM2255738", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP080353", null, null, "S6_F1.fq", "fastq", 490941500.0, 9818830.0, "GSM2255738 r1", "0:50", "A:119942635;C:111532763;G:133144810;T:126303825;N:17467", 50, null, null, null, 119942635, 111532763, 133144810, 126303825, 17467, "SRX1989728", "SRS1593550", "SRA446490", "GEO", "Wenzhou Medical University Chashan Campus Chashan University Town, Wenzhou, Zhejiang Province", 1, 1e-05, null, 0.0, null, 1.0, null, null, null, 50, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "China", "2016-07-29", "Larval", "Larval", "Trunk", "Surface Structure"]], "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": ["41251"], "units": {}, "query_ms": 12.322304999543121}