{"database": "metadata", "table": "run_metadata", "rows": [[57189, "SRR11263441", "SRX7870074", "SRS6278490", "SRP251978", "PRJNA611062", "Functional Characterization and Expression Analyses Show Differential Roles of Maternal and Zygotic Dgcr8 in Early Embryonic Development [miRNA seq]", "GSE146605", "Transcriptome Analysis", "Expression Analyses Show Differential Roles of Maternal and Zygotic Dgcr8 in Early  Embryonic Development Overall design: Methods: Embronic miRNA expression of 4.5 hpf wild type WT and maternal zygotic mutant MZdgcr8 zebrafish were generated by deep sequencing  in triplicate.", "parent bioproject:PRJNA611061", null, null, "miRNA of Wild type 3", "GSM4396429", null, "source name:Embryo|strain:AB|tissue:embryo|age:4.5hpf|genotype:wild type", "miRNA of Wild type 3", "Subsequently  unique sequences with length in 1825 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p  and 5p  derived miRNAs. Length variation at both three prime and five prime 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 22.0 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 genomes  and the hairpin RNA structures containing sequences were predicated from the flank 120 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 \u226412 2 number of base pairs in the stem region of the predicted hairpin \u226516 3 cutoff of free energy kCal/mol \u2264 15 4 length of hairpin up and down stems + terminal loop \u226550 5 length of hairpin loop \u2264200. 6 number of nucleotides in one bulge in mature region \u22644 7 number of biased errors in one bulge in mature region \u22642 8 number of biased bulges in mature region \u22642 9 number of errors in mature region \u22644 10 number of base pairs in the mature region of the predicted hairpin \u226512 11 percent of mature in stem \u226580. Supplementary files format and content: excel expression profiles", "Embryo", null, "small RNA was extracted from MZdcgr8 and Wild type embryos  50 embryos per sample at zfs:0000015 stage of early development representing 4.5 hpf using miRNeasy Mini Kit Qiagen. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "strain:AB|tissue:embryo|age:4.5hpf|genotype:wild type", "GSM4396429", "GSM4396429: miRNA of Wild type 3; Danio rerio; miRNA Seq", "GSM4396429", null, "1", "small RNA was extracted from MZdcgr8 and Wild type embryos  50 embryos per sample at zfs:0000015 stage of early development representing 4.5 hpf using miRNeasy Mini Kit Qiagen. RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM4396429", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP251978", null, null, "WT_3_miRNA.fq.gz", "fastq", 688929450.0, 13778589.0, "GSM4396429 r1", "0:50 1:0", "A:171239999;C:140558088;G:209452609;T:167641448;N:37306", 50, 0, null, null, 171239999, 140558088, 209452609, 167641448, 37306, "SRX7870074", "SRS6278490", "SRA1052219", "GEO", "The Chinese University of Hong Kong", 1, 0.00247, null, 0.00016, null, 0.99797, null, 0.60356, null, 50, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "5prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-03-08", "Blastula", "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": ["57189"], "units": {}, "query_ms": 11.421937997511122}