Project description:miRNA expression profile Keywords: small RNA profiling by high throughput sequencing The small RNA fraction (18-30nt) was cloned and sequenced from total RNA of each cell line
Project description:Comparison of miRNA expression profiles in a small set of prostate needle core biopsies or fine needle aspirates. Keywords: Expression profiling of prostate needle core biopsies
Project description:We report the high-throughput profiling of small RNA in extracellular vesicles (EVs) and their producing mammalian cells using Illumina small RNA sequencing platform. By obtaining over 2190 miRNA expression from 18 samples, the miRNA profile in EVs and their producing cells were compared. Results provide insight into gene profile difference between EV loading and the producing cells.
Project description:Time-dependent profile of differentially expressed miRNA following HIV-1 infection. Small RNAs were extracted from HIV-1 infected and non-infected pNL4-3 Jurkat cells at days 0, 7, 21 and 42 and miRNA expression was analyzed by microarray. Keywords: time course
Project description:Micro (mi)RNAs are small non-coding RNAs with key regulatory functions. Recent advances in the field allowed researchers to identify their targets. However, much less is known regarding the regulation of miRNA themselves. The accumulation of these tiny regulators can be modulated at various levels during their biogenesis from the transcription of the primary transcript (pri-miRNA) to the stability of the mature miRNA. Here, we studied the importance of the pri-miRNA secondary structure for the regulation of mature miRNAs accumulation. To this end, we used the Kaposi’s sarcoma herpesvirus, which encodes a cluster of twelve pre-miRNAs. Using small RNA profiling and quantitative northern blot analysis, we measured the absolute amount of each mature miRNAs in different cellular context. We found that the difference in expression between the least and most expressed viral miRNA could be as high as 60-fold. Using high-throughput selective 2’-hydroxyl acylation analyzed by primer extension (hSHAPE), we then determined the secondary structure of the long primary transcript. We found that highly expressed miRNAs derived from optimally structured regions within the pri-miRNA. Finally, we confirmed the importance of the local structure by swapping stem-loops for highly and lowly expressed miRNAs, which resulted in a perturbed accumulation of the mature miRNA.
Project description:Time-dependent profile of differentially expressed miRNA following HIV-1 infection. Small RNAs were extracted from HIV-1 infected and non-infected pNL4-3 Jurkat cells at days 0 and 21 and miRNA expression was analyzed by microarray. Keywords: time course
Project description:The 22Rv1 and PC-3 cells were transduced with shMIMIC human lentiviral vectors (Horizon Discovery, Cambridge, UK) to stably overexpress miRNA-23c or -4328. The SMARTvector Non-Targeting Control (NTC) was expressed to serve as a negative control. The vectors contained a turbo green fluorescent protein (turboGFP) and a puromycin resistance gene cassette. After transduction, cells were cultured in a medium supplemented with 5 µg/mL puromycin (Takara Bio, Tokyo, Japan) for antibiotic selection. Overexpression was confirmed by monitoring the turboGFP by fluorescence microscopy and by RT-qPCR analysis of miRNA-23c and -4328 levels. Relative protein quantification was performed to compare protein expression in 22Rv1 and PC-3 single cell clones overexpressing miRNA-23c and -4328, compared to corresponding NTC cells. Single cell clones overexpressing either miRNA-23c (n = 3), -4328 (n = 3) or NTC (n = 3) were analyzed in triplicate.
Project description:We sequenced 14 mouse tissues' small RNA samples from C57BL/6J mouse and aligned the sequenced reads to miRBase_v16 to profile miRNA expression levels in these 14 tissues.