run_metadata: 38256
This data as json
| 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 |
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| 38256 | SRR1596061 | SRX719267 | SRS715451 | SRP048591 | PRJNA262865 | Identification and Characterization of MicroRNAs in Zebrafish Spermatozoa by Illumina Sequencing | GSE61984 | Other | MicroRNAs miRNAs are involved in nearly every biological process examined to date. Mounting evidence show that some spermatozoa specific miRNAs play important roles in the regulation of spermatogenesis and germ cells development but little is known of the exact identity and function of miRNA in sperm cells or their potential involvement in spermatogenesis and germ cells development. Here we investigated the spermatozoa miRNA profiles using illumina deep sequencing combined with bioinformatic analysis using zebrafish as a model system. Deep sequencing of small RNAs yielded 12 million raw reads from zebrafish spermatozoa. Analysis showed that the noncoding RNA of the spermatozoa included tRNA rRNA snRNA snoRNA and miRNA. By mapping to the zebrafish genome we identified 400 novel and 204 conserved miRNAs which could be grouped into 104 families including zebrafish specific families such as mir 731 mir 724 mir 725 mir 729 and mir 2185. We report the first characterization of the miRNAs profiling in zebrafish spermatozoa. The obtained spermatozoa miRNAs profiling will serve as valuable resources to systematically study spermatogenesis in fish and vertebrate. Overall design: Examination of small RNA populations in zebrafish spermatozoa | pubmed:26418264 | zebrafish sperm | GSM1517943 | tissue:Zebrafish Spermatozoa|cell type:Spermatozoa|strain:AB wild type | zebrafish sperm | The sequencing data were analyzed as described previously by Xu et al 2014. The low quality reads were filtered to remove reads without xxx 3’ adaptor 5’ adaptor contaminant reads reads without xxx insert fragment reads containing polyA stretches and reads of less than 18 nt. Next the remaining sequences clean reads were mapped to the zebrafish genome using SOAP with a tolerance of one mismatch to analyze their distribution The sequences were aligned against known miRNA precursors and mature miRNAs deposited in the miRBase 20.0 to identify conserved miRNAs. The clean reads were compared against the sRNAs rRNAs tRNAs snRNAs snoRNA miRNA deposited in the GenBank and Rfam http://www.sanger.ac.uk/resources/databases/rfam.html databases to annotate the sRNA sequences. Because some sRNA tags might map to more than one category we used priority rules to ensure that every unique sRNA was mapped to only one annotation as follows: rRNA etc. GenBank >Rfam >known miRNA >repeat >exon >intron. Genome build: miRBase 20.0 Supplementary files format and content: zebrafish miRNA count.txt include RPKM values of each known miRNA in this sample | Zebrafish Spermatozoa | Total RNA was isolated from sample using Trizol reagent Invitrogen USA in accordance with the manufacturer’s protocol. RNA integrity was confirmed using the 2100 Bioanalyzer Agilent Technologies. RNA samples that passed the quality check were sent to BGI Shenzhen China for sRNA library construction and Solexa sequencing using standard protocols on the Illumina Hiseq 2000 platform. | cell type:Spermatozoa|strain:AB wild type | GSM1517943 | GSM1517943: zebrafish sperm; Danio rerio; miRNA Seq | GSM1517943 | 1 | Total RNA was isolated from sample using Trizol reagent Invitrogen USA in accordance with the manufacturer’s protocol. RNA integrity was confirmed using the 2100 Bioanalyzer Agilent Technologies. RNA samples that passed the quality check were sent to BGI Shenzhen China for sRNA library construction and Solexa sequencing using standard protocols on the Illumina Hiseq 2000 platform. | GEO Accession:GSM1517943 | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP048591 | zebrafish-sperm5.fq.bz2 | fastq | 588000000.0 | 12000000.0 | GSM1517943 r1 | 0:49 | A:122673394;C:136175879;G:140377184;T:188702650;N:70893 | 49 | 122673394 | 136175879 | 140377184 | 188702650 | 70893 | SRX719267 | SRS715451 | SRA188511 | GEO | SUN YAT-SEN UNIVERSITY | 1 | 2e-05 | 0.0 | 0.99997 | 1.0 | 49 | T | under 1.2% mapping rate | illumina | hiseq_era | unknown | size_fractionation | unknown | bulk | unknown | unknown | China | 2014-10-02 | Zygote | Embryo | Oocyte | Reproductive System |