Project description:We developed the microfluidic-oscillatory-washing-based ChIP-Seq (MOWChIP-Seq) protocol. We achieved genome-wide mapping of histone modifications (H3K4me3 and H3K27ac) with as few as 100 cells. Moreover, the automated microfluidic platform dramatically reduced assay time and has a potential for future scale-up.
Project description:Microfluidic devices provide a low-input and efficient platform for single-cell RNA-seq (scRNA-Seq). Here we present microfluidic diffusion-based RNA-seq (MID-RNA-seq) for conducting scRNA-seq with a diffusion-based reagent swapping scheme. This device incorporates cell trapping, lysis, reverse transcription and PCR amplification all in one microfluidic chamber. MID-RNA-Seq provides high data quality that is comparable to existing scRNA-seq methods while implementing a simple device design that permits multiplexing. The robustness and scalability of MID-RNA-Seq device will be important for transcriptomic studies of scarce cell samples.
Project description:We established a platform for the brain organoid culture by using human decellularized brain extracellular matrix (BEM) and a microfluidic device. This engineering concept of reconstituting brain-mimetic microenvironments facilitates development of a reliable culture platform for brain organoids, enabling effective modeling and drug development.
Project description:Immunoassays have been used for decades in clinical laboratories to quantify proteins in serum/plasma samples. However, different limitations hinder their use in some cases. Mass spectrometry (MS)-based proteomics analysis has recently appeared as a promising option to assess panels of protein biomarkers and provide protein profiles useful for health state monitoring. Nevertheless, translation of MS-based proteomics into the clinics is still hampered by the complexity, the substantial time and human workforce necessary for sample preparation. The processing of plasma matrix is especially tricky as it contains more than 3000 proteins spanning in an extreme dynamic range (10e10) of concentrations. To address this pre-analytical challenge, we have conceived a microfluidic device (PepS) to automate and accelerate blood sample preparation for bottom-up MS-based proteomic analysis. The microfluidic cartridge is operated through a dedicated compact instrument providing fully automated fluid processing and thermal control. In less than 2 hours, PepS device enables whole blood collection at the bedside, plasma separation and calibration, depletion of albumin, protein digestion with trypsin and stabilization of tryptic peptides on solid phase extraction sorbent. The performance of PepS device was assessed using discovery proteomics and targeted proteomics on a panel of three protein biomarkers routinely assayed in clinical laboratories. This innovative microfluidic device and associated instrumentation is expected to streamline and simplify clinical proteomic studies.
Project description:Chemoresistance is a major cause of treatment failure in many cancers. However, the lifecycle of cancer cells as they respond to and survive environmental and therapeutic stress isunderstudied. In this study, we utilized a microfluidic device to induce the development ofdoxorubicin-resistant (DOXR) cells from triple negative breast cancer (TNBC) cells within 11days by generating gradients of DOX and medium. In vivo chemoresistant xenograft models,an unbiased genome-wide transcriptome analysis, and a patient data/tissue analysis allshowed that chemoresistance arose from failed epigenetic control of the nuclear protein-1(NUPR1)/histone deacetylase 11 (HDAC11) axis, and high Nupr1 expression correlated withpoor clinical outcomes. These results suggest that the chip can rapidly induce resistant cellsthat increase tumor heterogeneity and chemoresistance, highlighting the need for furtherstudies on the epigenetic control of the NUPR1/HDAC11 axis in TNBC.
Project description:Investigation in bacterial transcriptomics is widely used to investigate gene regulation, bacterial susceptibility to antibiotics, host-pathogen interactions, and pathogenesis. Transcriptomics is crucially dependent on suitable methods to isolate and detect bacterial RNA. Microfluidic approaches offer ways of creating integrated point-of-care systems, analysing a sample from preparation, RNA isolation through to detection. Critical for on-chip diagnostics to deliver on their promise is that mRNA expression is not altered through the use microfluidic sample processing. Here, we investigate the impact on the use of a microfluidic sample processing system based on hydrodynamic separation upon RNA expression of bacteria isolated from blood to prove its suitability for further microfluidic test development. A 10 array study using total RNA recovered from bacteria isolated using the microfluidic device and total RNA recovered from bacteria that were not separated using the device were compared. Arrays were performed in 5 biological replicates from each condition
Project description:Global untargeted metabolomics study to analyse culture media extracted from an innovative microfluidic device or traditional microdrops in presence or absence of murine embryos to investigate PDMS-release of biomolecules and embryo metabolic activity.