A platform for coupling chromatin profiling with single cell transcriptomics

PROJECT SUMMARY The development and commercialization of microfluidic based single cell RNA seq platforms has enabled the transcriptomes of thousands of single cells to be profiled at a timeallowing researchers to differentiate between cell types and study cell fate decisionsHowevernone of these new technologies can correlate single cell genetic or epigentic variations with gene expression at high throughputFundamentallycurrent microfluidic technologies are either too inflexible to perform multiple types of sequencing on the same single cellor are too low throughput to address many biological questionsWe will overcome this limitation by utilizing a new microfluidic technologyPrinted Droplet Microfluidicsto build a platform to perform high throughput single cell multi omicsPrinted Droplet Microfluidics utilizes a unique droplet microfluidic print head that serves as a deterministic single cell and droplet printerand allows nanoliter scale fluidic manipulations to be performed in an array formatincluding multiple protocols on the same single cell lysateIn this projectwe will build a platform to perform chromatin accessibilityATAC seqand transcriptome sequencing onsingle cellsIn Specific Aimwe will adapt a single cell RNA seq protocol to the printed droplet arrayand develop methods to identify the original geographic location of a cell in the RNA seq dataIn Specific Aimwe will develop a high throughput single cell ATAC seq protocol in an array formatwith methods again being developed to positionally label single cell ATAC seq dataAchievement of these aims will prove that multiple single cell sample preparation protocols can be linked together and performed on the same single cell lysateA proposed phase II project would involve full integration RNA seq and ATAC seq protocolsscaling throughput andgtsingle cellsand early productization of the hardware and disposables PROJECT NARRATIVE The availability of single cell sequencing technologies has enabled a paradigm shift in the study of cellular heterogeneityand an improved understanding of fundamental biologyHoweverthe ability to correlate genetic or epigenetic mutations to changes in transcription levels in large number of single cells does not existleading to a large gap in the study of gene expressionWe will apply Scribe Biosciencesproprietary Printed Droplet Microfluidics technology to develop a platform for coupled epigenetic and transcriptomic sequencing of thousands of single cells