Project description:Using 3' droplet-based single-cell sequencing, we performed the transcriptional profiling of mouse large intestinal epithelial cells at the single-cell level.
Project description:Using 3' droplet-based single cell sequencing, we profiled single cells derived from a fresh human small intestinal epithelial tissue and human small intestinal organoids cultured with either IGF1/FGF2 or EGF/p38i.
Project description:Here, we introduce an in-silico algorithm demuxlet that harnesses naturally occurring genetic variation in a pool of cells from unrelated individuals to discover the sample identity of each cell and identify droplets containing cells from two different individuals (doublets). These two capabilities enable a simple multiplexing design that increases single cell library construction throughput by experimental design where cells from genetically diverse samples are multiplexed and captured at 2-10x over standard workflows. We further demonstrate the utility of sample multiplexing by characterizing the interindividual variability in cell type-specific responses of ~15k PBMCs to interferon-beta, a potent cytokine. Our computational tool enables sample multiplexing of droplet-based single cell RNA-seq for large-scale studies of population variation and could be extended to other single cell datasets that incorporate natural or synthetic DNA barcodes.
Project description:Using 5' droplet-based single cell sequencing, we profiled single cells dervied from human colorectal cancer organoids carrying either APC mutation or RSPO fusion, and paired normal colon organoids for the later.
Project description:In this study, we introduce BacDrop, a bacterial droplet-based high throughput scRNA-seq technology that can be applied to large cell numbers. We applied BacDrop to study Klebsiella pneumoniae clinical isolates and elucidated their critical, genome-wide heterogeneity in the absence and presence of antibiotic perturbations.
Project description:In this project we profiled small intestinal epithelium, lamina propria immune cells as well as intraepithelial immune cells from 5-weeks old WT mice derived from Jackson laboratories and littermate colonized with segmented filamentous bacteria (SFB) 2 weeks prior to analysis, using 10x droplet-based single-cell RNA sequencing.