Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Next generation sequencing of small RNAs isolated from exosomes in human semen

ABSTRACT: Preparation of exosomes isolated from semen contain a substantial amount of RNA, mostly from 20 to 100 nucleotides in length. We sequenced separately 20-40 and 40-100 nucleotide fractions of RNA from exosomes isolated from semenal fluid from six healthy donors. We found various classes of small non-coding RNA, including mature microRNA and piwi-RNA, as well as abundant Y RNAs and tRNAs present in both full length and fragmented forms. Specific RNAs were consistently present in all donors. For example, fifteen (of ~2,600 known) microRNAs constituted over 80% of mature microRNA in SE. Additionally, tRNA fragments were strongly enriched for 5M-bM-^@M-^Y-ends of 18-19 or 30-34 nucleotides in length. Size-fractionated small RNA profiles from exosomes isolated from the seminal fluid of six healthy donors

ORGANISM(S): Homo sapiens

SUBMITTER: Sangsoon Woo

PROVIDER: E-GEOD-56076 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Exosomes in human semen carry a distinctive repertoire of small non-coding RNAs with potential regulatory functions.

Vojtech Lucia L Woo Sangsoon S Hughes Sean S Levy Claire C Ballweber Lamar L Sauteraud Renan P RP Strobl Johanna J Westerberg Katharine K Gottardo Raphael R Tewari Muneesh M Hladik Florian F

Nucleic acids research 20140516 11

Semen contains relatively ill-defined regulatory components that likely aid fertilization, but which could also interfere with defense against infection. Each ejaculate contains trillions of exosomes, membrane-enclosed subcellular microvesicles, which have immunosuppressive effects on cells important in the genital mucosa. Exosomes in general are believed to mediate inter-cellular communication, possibly by transferring small RNA molecules. We found that seminal exosome (SE) preparations contain ...[more]

PMID: 24838567

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Project description:Purpose: The study focused on the RNA content of supportive (AFT024) and non supportive (BFC012) stromal lines and their respective exosomes to analyze the molecular complexity of the Hematopoietic Stem and Progenitor Cell niche Methods: All the samples from small RNA (SR) and polyA-RNA libraries were sequenced using 1Ã50 bp single reads high-throughput sequencing (RNA-Seq) in single lane on Illumina HiSeq 2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks and by Fisher's test for polyA-RNA, or with bowtie and parse tools for smallRNA (galaxy server https://lbcd41.snv.jussieu.fr/). Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm10). We focused on differentially expressed transcripts between i) exosomes from supportive and non supportive stromal cells and ii) exosomes and their respective cells.Using a subtractive strategy, we identified 324 mRNAs and 23 miRNAs specific to the exosomes of the supportive stromal line AFT024. We used gene ontology annotation to study the biological functions associated to these specific gene sets. Transcripts involved in negative regulation of apoptosis were found enriched in AFT exosomes. Conclusions: Our RNA seq analysis combined with biological assays reveal that exosomes serve as an important and novel mediator for the HSPC supporting capacity of stromal cells. This unprecedented effort to resolve the molecular complexity of the HSPC-targeted exosomes, provide new candidat genes of the HSPC support and may help designing innovative stromal-free culture conditions to deliver specific molecules to HSPCs. Fetal liver derived stromal lines and their corresponding secreted exosomes were sequenced using Illumina HiSeq2500 technology (Fasteris, CH). Due to low amount of exosomal RNAs, several RNA extraction were pooled and split to perform 2 technical sequencing replicates that were merged during bionformatic analyses.

Dataset Information

Next generation sequencing of small RNAs isolated from exosomes in human semen

Publications

Exosomes in human semen carry a distinctive repertoire of small non-coding RNAs with potential regulatory functions.

Similar Datasets

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