Abstract: Disclosed herein include methods, devices, kits, and systems for nucleic acid sequencing, for example, to determine cell-cell interaction using a dielectrophoresis microfluidic device.

Abstract: Disclosed herein include methods, systems, compositions and kits for determining cell-cell interaction, for example, using nucleic acid sequencing. The method can match a cell barcode sequence associated with a cell of a plurality of cells with a cell barcode sequence associated with a partition of a plurality of partitions to identify the partition the cell has originated from in the plurality of partitions. In some embodiments, a pair of interacting cells within a partition are attached with a common cell barcode. The nucleic acid sequences of the pair of interacting cells having the common cell barcode can be tracked to the partition the pair of interacting cells has originated from, where phenotypic observables of the interacting cells can be obtained, for example, using optical imaging, thereby linking cell nucleic acid sequences such as expression profiles to cell functionality and the nature of the cell-cell interaction.

Abstract: Methods and systems for the high throughput RNA profiling or sequencing analysis of fixed single cells are provided. The methods and systems utilize barcoded microcarriers comprising a small carrier bead attached to a plurality of molecular barcodes with cleavable linkers, wherein these barcoded microcarriers are then combined in a system (e.g., a sealed system) with a single cell. The molecular barcodes are then released from the carrier beads to anneal to the mRNAs in the cells. Using reverse transcription, barcoded cDNAs is then generated from the mRNAs and the cells are lysed or digested to release the barcoded cDNAs for sequencing.