A long-sought milestone in microfluidics research has been the development of integrated technology for scalable analysis of transcription in single cells. Here we present a fully integrated microfluidic device capable of performing high-precision RT-qPCR measurements of gene expression from hundreds of single cells per run. Our device executes all steps of single-cell processing, including cell capture, cell lysis, reverse transcription, and quantitative PCR. In addition to higher throughput and reduced cost, we show that nanoliter volume processing reduced measurement noise, increased sensitivity, and provided single nucleotide specificity. We apply this technology to 3,300 single-cell measurements of ( i ) miRNA expression in K562 cells, ( ii ) coregulation of a miRNA and one of its target transcripts during differentiation in embryonic stem cells, and ( iii ) single nucleotide variant detection in primary lobular breast cancer cells. The core functionality established here provides the foundation from which a variety of on-chip single-cell transcription analyses will be developed.

a b s t r a c tWe study the velocity and shape of air bubbles rising through a transparent yield-stress fluid. The bubbles are small enough compared to the experimental vessel that effects of walls are weak. We find that the terminal rise velocity of the bubbles increases approximately linearly with bubble radius over the range of volumes accessible in our experiments. We observe bubble motion only when the bubbles are larger than a certain critical radius. In terms of a dimensionless yield parameter Y, the ratio between the force due to the yield stress and the buoyant force, we observe bubble motion only for Y 0.50 ± 0.04. The bubbles are non-spherical, having the shape of an inverted teardrop with a rounded head and a cusp-like tail. The cusps may be an indication that elasticity plays a significant role in this system. By fitting the cross-sectional radius of the bubble as a function of the axial coordinate to an empirical function, we study the dependence of the bubble shape on volume and the yield stress of the material.

We study the motion of a sphere falling through soft viscoelastic materials when the time scale of the motion is short compared to the elastic relaxation time of the material. We observe shocks generated by the passage of the sphere at Mach numbers greater than 1. The sphere can undergo oscillations before reaching a steady terminal speed, and we show that these oscillations have the same frequency as the shear wave associated with the shock.

We study the behavior of a yield-stress fluid following the impact of a vertically falling sphere. Since the impact produces shear stresses larger than the yield stress, the material in the vicinity of the impact becomes fluidized. The sphere entrains air when it enters the fluid, and the resulting cavity pinches off below the surface. The upper part of this cavity then rebounds upward. For sufficiently fast impacts, a vertical jet is produced by the cavity collapse. While many aspects of this process are similar to that in Newtonian fluids or granular materials, the rheological properties of our target material change the scaling of the cavity pinch-off depth and have a dramatic effect on the height of the jets. The material returns to a solid-like behavior once the stresses due to the impact have relaxed to below the yield stress, leaving a crater in the surface of the material. We find that the diameter of this crater depends nonmonotonically on the impact speed. The crater shape also changes with speed, reflecting the dynamics of the impact process.