Split microchip for single cell transcriptome and proteome analysis

Given vast heterogeneity of immune cells, searching for gene expression and transcriptional networks belonging to specific cellular functions such as cytokine production has been challenging. To overcome this limitation, researchers at SUNY Albany developed a splittable single-cell microchip that integrates a high-density antibody array for cytokine protein detection, while the same single cells with protein profiles can be subsequently sequenced to obtain the genome-wide transcriptome. Combined with bioinformatics algorithms, the researchers discovered a subgroup of highly coexpressed genes correlating with TNFα secretion in mouse macrophage cells. This technology and the data analysis may lead to an unprecedented understanding of regulation mechanisms of the immune system and have the potential to impact disease treatment and drug discovery.

Scheme of detecting both secreted proteins and
transcriptome from the same single cells


The PDMS part of the microchip is coated with collagen and is seeded with single cells. Subsequently, the microchambers are sealed with an antibody array for capturing secreted cytokines. Then the microchip is split for ELISA protein detection and cell imaging separately. Single cells with a protein profile are picked up by a 32G syringe and lysed immediately for next generation sequencing (NGS) of mRNAs. The image in step 5.1 is a typical result after detection, with each row corresponding to a single cell microchamber. Detected proteins are in red color and the reference is in green color. The arrow in step 5.2 indicates a fluorescent cell captured by the syringe needle.

George J, Wang J. (2016) Assay of Genome-Wide Transcriptome and Secreted Proteins on the Same Single Immune Cells by Microfluidics and RNA Sequencing. Anal Chem 88(20):10309-10315. [abstract]

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