Single-cell genome, DNA methylome, and transcriptome sequencing methods have been separately developed. However, to accurately analyze the mechanism by which transcriptome, genome and DNA methylome regulate each other, these omic methods need to be performed in the same single cell. Here we demonstrate a single-cell triple omics sequencing technique, scTrio-seq, that can be used to simultaneously analyze the genomic copy-number variations (CNVs), DNA methylome, and transcriptome of an individual mammalian cell. We show that large-scale CNVs cause proportional changes in RNA expression of genes within the gained or lost genomic regions, whereas these CNVs generally do not affect DNA methylation in these regions. Furthermore, we applied scTrio-seq to 25 single cancer cells derived from a human hepatocellular carcinoma tissue sample. We identified two subpopulations within these cells based on CNVs, DNA methylome, or transcriptome of individual cells. Our work offers a new avenue of dissecting the complex contribution of genomic and epigenomic heterogeneities to the transcriptomic heterogeneity within a population of cells.

We combine fiber Bragg grating (FBG) technology with a wet chemical etch-erosion procedure and demonstrate two types of refractive index sensors using single-mode optical fibers. The first index sensor device is an etch-eroded single FBG with a radius of $3\mu \mathrm{m}$ , which is used to measure the indices of four different liquids. The second index sensor device is an etch-eroded fiber Fabry-Pérot interferometer (FFPI) with a radius of $\sim 1.5\mu \mathrm{m}$ and is used to measure the refractive indices of isopropyl alcohol solutions of different concentrations. Due to its narrower resonance spectral feature, the FFPI sensor has a higher sensitivity than the FBG sensor and can detect an index variation of $1.4\times {10}^{-5}$ . Since we can measure the reflection signal, these two types of sensors can be fabricated at the end of a fiber and used as point sensors.

Circular RNAs (circRNAs) are a new class of non-polyadenylated non-coding RNAs that may play important roles in many biological processes. Here we develop a single-cell universal poly(A)-independent RNA sequencing (SUPeR-seq) method to sequence both polyadenylated and non-polyadenylated RNAs from individual cells. This method exhibits robust sensitivity, precision and accuracy. We discover 2891 circRNAs and 913 novel linear transcripts in mouse preimplantation embryos and further analyze the abundance of circRNAs along development, the function of enriched genes, and sequence features of circRNAs. Our work is key to deciphering regulation mechanisms of circRNAs during mammalian early embryonic development.

We use the coupling matrix formalism to investigate continuous-wave and pulse propagation through microring coupled-resonator optical waveguides (CROWs). The dispersion relation agrees with that derived using the tight-binding model in the limit of weak inter-resonator coupling. We obtain an analytical expression for pulse propagation through a semi-infinite CROW in the case of weak coupling which fully accounts for the nonlinear dispersive characteristics. We also show that intensity of a pulse in a CROW is enhanced by a factor inversely proportional to the inter-resonator coupling. In finite CROWs, anomalous dispersions allows for a pulse to propagate with a negative group velocity such that the output pulse appears to emerge before the input as in “superluminal” propagation. The matrix formalism is a powerful approach for microring CROWs since it can be applied to structures and geometries for which analyses with the commonly used tight-binding approach are not applicable.