Abstract: Systems and methods for associating single cell imaging data with RNA transcriptomics. Single cells are isolated into microwells with a microbead having oligonucleotides conjugated on its surface. Each oligonucleotide includes a cell identifying optical barcode that is unique to that bead and binding sequence for RNA capture after cell lysis. The system is configured for loading single cells into the microarray and for flowing cell lysis buffers and other reagents into the microarray for performing RNA library sample preparation. The system is also configured for lowing optical hybridization probes that are complementary to the cell identifying optical barcodes and optically labeled onto the microwell array and for obtaining images of the microwells in response to the probes. The system and unique cell identifying optical barcodes and complementary optical hybridization probes facilitate a link between phenotypic imaging of cells resident on the microwell array with single cell whole transcriptome sequencing.

Abstract: A method to extract, amplify and separate nucleic acid in a microfluidic device having a plurality of chambers and channels can include a) introducing cells having nucleic acid to a first chamber of the microfluidic device and subjecting the cells in the first chamber to conditions that lyse the cells. The method can further include b) subjecting the first chamber to centrifugal force, thereby allowing the lysate or a portion thereof having nucleic acid to be distributed to a second chamber through a first channel in the microfluidic device. The method can also include c) combining the lysate or the portion thereof and reagents for amplification of the nucleic acid, thereby providing a second mixture. The method can also include d) subjecting the second chamber to centrifugal force, thereby allowing gas to be expelled from the second mixture.

Abstract: A method to extract, amplify and separate nucleic acid in a microfluidic device having a plurality of chambers and channels can include a) introducing cells having nucleic acid to a first chamber of the microfluidic device and subjecting the cells in the first chamber to conditions that lyse the cells. The method can further include b) subjecting the first chamber to centrifugal force, thereby allowing the lysate or a portion thereof having nucleic acid to be distributed to a second chamber through a first channel in the microfluidic device. The method can also include c) combining the lysate or the portion thereof and reagents for amplification of the nucleic acid, thereby providing a second mixture. The method can also include d) subjecting the second chamber to centrifugal force, thereby allowing gas to be expelled from the second mixture.

Abstract: This disclosure provides for apparatuses, systems and methods for in vitro sample detection. For example in one embodiment, this disclosure provides an automated Pe-toner microfluidic device (and related method) on a centrifugal platform for DNA sample lysis and DNA extraction. A second embodiment provides a system and method for qualitative detection, quantification, and real-time monitoring of nucleic acid amplification products using magnetic bead aggregation inhibition. A third embodiment provides a platform for simultaneous detection of mRNA markers from blood, cell-free semen, sperm, saliva, and vaginal fluid. The third embodiment comprises a system and method that provide for simple, rapid, and fluorescence-free detection of body fluids using mRNA marker amplification and optical detection for mRNA marker analysis with a smart phone with image analysis.

Abstract: A method to extract, amplify and separate nucleic acid in a microfluidic device having a plurality of chambers and channels can include a) introducing cells having nucleic acid to a first chamber of the microfluidic device and subjecting the cells in the first chamber to conditions that lyse the cells. The method can further include b) subjecting the first chamber to centrifugal force, thereby allowing the lysate or a portion thereof having nucleic acid to be distributed to a second chamber through a first channel in the microfluidic device. The method can also include c) combining the lysate or the portion thereof and reagents for amplification of the nucleic acid, thereby providing a second mixture. The method can also include d) subjecting the second chamber to centrifugal force, thereby allowing gas to be expelled from the second mixture.