This is a collection of our publications that give a good overview of what we are able to do for your project.
Morten's Venø's Favorites:
Temporal lobe epilepsy is a common type of epilepsy and many of the patients develop resistance to available anti-epileptic drugs. In this study, the role of circRNA was explored by RNA-seq of hippocampal tissue from epilepsy model rats. RNA-seq experiments were performed by omiics team members, including bioinformatics analysis by Morten Venø. This revealed 218 significantly differentially regulated circRNA, two of which were further validated and linked to regulation of specific miRNAs, revealing a potential role for aberrant circRNA expression in the neural circuitry of the epileptic brain.
Morten Venø et al. comprehensively sequenced small RNAs in hippocampus from three different epileptic rodent model systems at timepoints during development of epilepsy and after onset of chronic epilepsy. The omiics core team performed Ago immune precipitation followed by small RNA sequencing and Morten did the small RNA bioinformatics resulting in discovery of a set of miRNAs with consistent epileptic deregulation in all rodent models. Antagomir inhibition of these miRNAs had antiseizure effect in model animals, due to derepression of the TGF-β signaling pathway. This comprehensive study revealed a set of miRNAs that are high value therapeutic antiseizure targets.
SMARTer single cell total RNA sequencing. Nucleic Acids Res. 2019
In this study, SMARTer stranded single cell total RNA sequencing (Takara) was performed on cancer cell lines. This type of sequencing generates full gene coverage single cell RNA-seq without performing poly-A purification, which allows detection of non-poly-A RNAs such at circRNAs. Morten Venø performed circRNA detection for the single cell RNA-seq data. This is a proof-of-principal paper showing the prospects of doing total RNA-seq on single cells.
Yan Yan's Favorites:
In this paper, Yan et al. characterized the extracellular vesicles (EVs) released from multipotent stem cells (MSCs) during osteoblastogenesis and profiled small non-coding RNAs EVs using small RNA sequencing. With the comprehensive data analysis done by omiics, it was found that the EVs contained a specific subset of microRNAs (miRNAs) and tRNA-derived small RNAs (tsRNA) compared to their parental cells, and osteoblastic differentiation had an effect on the small RNA profiles of MSC-EVs. You can actually see a video and learn more about the methods in a companion JoVE publication
Comprehensive analysis of soluble RNAs in human embryo culture media and blastocoel fluid. Journal of Assisted Reproduction and Genetics, 2020.
In order to investigate the biomarkers of embryo viability, the small RNA sequencing was used to profile small non-coding RNA levels in spent and unconditioned embryo culture media. Yan optimized the protocol of sequencing library construction and Morten did the comprehensive data analysis. Interestingly, tiRNA fragments appear to be overexpressed in conditioned IVF media samples and could potentially be a novel biomarker worthy of investigation.
Ischemic exercise conducted as low-load blood flow restricted resistance exercise (BFRE) can lead to muscle remodeling and promote muscle growth, possibly through activation of muscle precursor cells. Cell activation can be triggered by blood borne extracellular vesicles (EVs) as these nano-sized particles are involved in long distance signaling. In this study, Yan isolated EVs from plasma of healthy human subjects performing a single bout of BFRE and did small RNA sequencing to profile the miRNAs in EVs. It was found that after BFRE, 12 miRNAs were significantly altered.
In this study, Yan used small RNA sequencing to profile miRNA expression in plasma collected from healthy human and oral cancer patient before and one year after surgery. It was found that the plasma miRNA expression was deregulated in patients and several miRNAs were associated with cancer recurrence.