Search

Resolving the spatial distribution of RNA and protein in tissues at subcellular resolution is a challenge in the field of spatial biology. We describe spatial molecular imaging, a system that measures RNAs and proteins in intact biological samples at subcellular resolution by performing multiple cycles of nucleic acid hybridization of fluorescent molecular barcodes. We demonstrate that spatial molecular imaging has high sensitivity (one or two copies per cell) and very low error rate (0.0092 false calls per cell) and background (~0.04 counts per cell). The imaging system generates three-dimensional, super-resolution localization of analytes at ~2 million cells per sample. Cell segmentation is morphology based using antibodies, compatible with formalin-fixed, paraffin-embedded samples. We measured multiomic data (980 RNAs and 108 proteins) at subcellular resolution in formalin-fixed, paraffin-embedded tissues (nonsmall cell lung and breast cancer) and identified18 distinct cell types, ten unique tumor microenvironments and 100 pairwise ligand-receptor interactions. Data on800,000 single cells and ~260 million transcripts can be accessed at http://nanostring.com/CosMx-dataset .

Circulating tumor cells (CTCs) are rare cancer cells that are shed from primary or metastatic tumors into the peripheral blood circulation. Phenotypic and genetic characterization of these rare cells can provide important information to guide cancer staging and treatment, and thus further research into their characteristics and properties is an area of considerable interest. In this protocol, we describe detailed procedures for the production and use of a label-free spiral microfluidic device to allow size-based isolation of viable CTCs using hydrodynamic forces that are present in curvilinear microchannels. This spiral system enables us to achieve ≥ 85% recovery of spiked cells across multiple cancer cell lines and 99.99% depletion of white blood cells in whole blood. The described spiral microfluidic devices can be produced at an extremely low cost using standard microfabrication and soft lithography techniques (2-3 d), and they can be operated using two syringe pumps for lysed blood samples (7.5 ml in 12.5 min for a three-layered multiplexed chip). The fast processing time and the ability to collect CTCs from a large patient blood volume allows this technique to be used experimentally in a broad range of potential genomic and transcriptomic applications.

Seasonal variations of baroclinic tides for K1 and M2 constituents were separately studied using two-dimensional numerical simulations along the 21°N section of the northern South China Sea (SCS). Results show that the continental slope of the northern SCS and the west ridge of the Luzon Strait are supercritical to K1 internal tides, which may be trapped in the deep basin of the SCS and form standing or partial standing waves. Meanwhile, these areas are sub-critical to M2 internal tides, which can transmit onto the shelf and are seldom reflected back into the basin. The trapped K1 internal tides are dominated by mode-2 and mode-3 in summer and by mode-1 and mode-3 in winter. Moreover, high mode K1 internal tides account for nearly 20–40 % of the total energy density in winter and 15–20 % in summer. The pattern of K1 internal tides in the basin is mainly determined by the percentage of reflected energy from the continental slope. The phase difference between the incoming mode-1 and mode-2 K1 internal tides near the continental slope are nearly out of phase in winter, which means that the percentage of reflection of the K1 internal tide is larger than that in summer. Both the convergence and high mode K1 internal tides can enhance the vertical shear. The above results indicate that, in the deep basin of the SCS, water mixing potentially induced by internal tides in winter is stronger than in summer.

The paper reports a new method for three-dimensional observation of the location of focused particle streams along both the depth and width of the channel cross-section in spiral inertial microfluidic systems. The results confirm that particles are focused near the top and bottom walls of the microchannel cross-section, revealing clear insights on the focusing and separation mechanism. Based on this detailed understanding of the force balance, we introduce a novel spiral microchannel with a trapezoidal cross-section that generates stronger Dean vortices at the outer half of the channel. Experiments show that particles focusing in such device are sensitive to particle size and flow rate, and exhibits a sharp transition from the inner half to the outer half equilibrium positions at a size-dependent critical flow rate. As particle equilibration positions are well segregated based on different focusing mechanisms, a higher separation resolution is achieved over conventional spiral microchannels with rectangular cross-section., United States. Defense Advanced Research Projects Agency. Dialysis-Like Therapeutics (SSC Pacific Grant N66001-11-1-4182)