Transcriptomic dissection of whole lymphoid organs using high throughput single cell sequencing.

Abstract Secondary lymphoid organs contain heterogeneous immune cell populations that play central roles in the defense against pathogens. Proper immune response relies on dynamic and complex changes in the composition and function of these immune cells. Until recently, high throughput single cell analysis was primarily achieved through flow cytometry, which is limited by the number of cell surface markers that can be examined simultaneously. But advances in single cell sequencing technology has made transcriptional profiling of single cells possible. In this study, we demonstrate the power of using the BDTM Resolve single cell sequencing platform to delineate immune cell types in mouse spleen and lymph node tissues. Using BDTM Resolve’s micro-well array and molecular indexing technology, we captured thousands of cells from disassociated mouse spleen and lymph nodes. Around 1000 cells were subsampled for single cell analysis using two approaches: whole transcriptome amplification(WTA) and targeted highly multiplexed PCR, which surveys over 400 immune relevant genes. Based on transcriptional profiles, we were able to reconstruct all the major immune cell compartments as well as rarer subsets using both assays. While WTA analysis offers an unbiased approach for identifying novel genes and pathways, our study shows that highly multiplexed PCR is a cost effective alternative for profiling immune population in tissues, requiring significantly fewer reads and achieving higher sensitivity for low abundance transcripts. The BDTM Resolve single cell system streamlines whole tissue immune profiling from thousands of cells, and can easily be applied to other tissues to understand immunological changes in cell composition and function.