Our pioneering technology uses combinatorial cDNA barcoding within cells themselves, and thus does not require complex cell partitioning instruments.
Individual transcriptomes are uniquely labeled by passing fixed cells or nuclei through four rounds of barcoding. In each round, pooled cells are randomly distributed into different wells, and transcripts are labeled with well-specific barcodes. Using next-generation sequencing, each transcriptome is assembled by combining reads containing the same four-barcode combination. Four rounds of barcoding can yield 3,538,944 possible barcode combinations (three rounds of barcoding in 48x96x96 wells followed by a fourth round with 8 PCR reactions), enough to uniquely label up to one hundred thousand cells while avoiding doublets.
Parse Biosciences offers a new strategy for single cell RNA sequencing that can profile up to 100,000 cells in parallel across up to 48 samples.
Profile up to 100,000 cells across up to 48 distinct cell samples. After fixation, cells or nuclei undergo four rounds of combinatorial barcoding. This yields a total of 48x96x96x8 possible barcode combinations, enough to uniquely profile up to 100,000 single cells. The Parse Biosciences Whole Transcriptome kits are a dramatic improvement on the original SPLiT-seq publication in terms of sensitivity of gene detection.
Parse Biosciences' fixation allows researchers to store single-cell or single-nucleus suspensions for up to 6 months. The ability to separate sample extraction from downstream barcoding could lead to significant time and cost savings. For example, biological samples at collected at inconvenient times of the day can be fixed and sequenced later. It is also possible to multiplex up to 48 samples collected at different time points and fixed; these fixed samples can then be run in parallel for cell barcoding. At the end of cell barcoding, the cells are divided into 8 sublibraries, with anywhere from 100 to 12,500 cells per sublibrary (8 sublibraries x 12,500 cells = 100,000 cells). Sublibraries can be processed and sequenced independently from one another, providing researchers the freedom to fractionate their data and adjust sequencing depth as they choose.
Traditional single cell RNA sequencing methods require complex equipment to first partition individual cells before barcoding RNA molecules in a cell-specific manner. Our Single Cell Whole Transcriptome kit requires only basic laboratory tools. By using cells themselves as compartments, we can employ a series of split-pooling steps to label all RNA molecules in a given cell with a unique combination of barcodes. This makes it possible for researchers to perform our standalone kits on their time without the need for upfront costs and instrumentation maintenance fees.