In this invention disclosure, we described a nanoscale sample preparation method and device to enable the parallel analysis of many different types of molecules in small amounts of biological samples, down to single cells. The main innovations are: 1. We developed a nanoliter dividing technology to parallelly splitting samples between two droplet arrays, which will be measured separately with different technology. 2. The technology involves two key steps: (1) merge of two droplet arrays to mix; (2) split the two droplet arrays to generate two chips for subsequent analysis. The overall workflow is shown in Figure 1. Single cells or a low number of cells are isolated into nanodroplets, followed by cell lysis to release intracellular molecules, such as RNA transcripts, proteins, and metabomics. At the same time, we load an array of blank droplets on a different chip. Next, we will align the two chips together to allow one-to-one droplet merging (figure 2). The assembled droplet chips will be incubated to allow efficient mixing between droplet pairs. Finally, the two chips are separated to split the merged droplet and divide molecules in the two chips. As an initial demonstration of the technology, we co-measured mRNA transcript and proteins using RNA sequencing and mass spectrometry methods, respectively. 3. The surface chemistry of two droplet array chips are adjusted to specifically enriching different types of molecules. The surface can be modified to be hydrophobic to enrich proteins from cell lysates; alternatively, the surface can be modified with poly-T oligos to enrich mRNA molecules. 4. The merge-and-split workflow can be performed for many cycles to enhance mixing and allow efficient enrichment on nanowell surfaces. 5. We demonstrated the method with integrated transcriptomics and proteomics of single cells. It can be applied to other omics analysis, such as mRNAs/metabolites; proteins/metabolites; intact proteins/digested proteins, etc.