A5050295892- Single-cell and spatial transcriptomics
- Microfluidic and Bio-sensing Technologies
- ATP Synthase and ATPases Research
- Mitochondrial Function and Pathology
- Reproductive System and Pregnancy
- Tryptophan and brain disorders
- Cancer Genomics and Diagnostics
- Cancer, Hypoxia, and Metabolism
- Gut microbiota and health
- Extracellular vesicles in disease
- Cell Image Analysis Techniques
Vanderbilt University
2022-2025
Vanderbilt University Medical Center
2022-2023
Pitzer College
2020
Droplet-based single-cell RNA-seq (scRNA-seq) data are plagued by ambient contaminations caused nucleic acid material released dead and dying cells. This is mixed into the buffer co-encapsulated with cells, leading to a lower signal-to-noise ratio. Although there exist computational methods remove post-hoc, reliability of algorithms in generating high-quality from low-quality sources remains uncertain. Here, we assess quality before filtering set quantitative, contamination-based metrics...
The structure and function of the mammalian gut vary by region, yet why inflammatory diseases manifest in specific regions not others remains unclear. We use a TNF–overexpressing Crohn′s disease (CD) model (Tnf ΔARE/+ ), which typically presents terminal ileum (TI), to investigate how environmental factors interact with host′s immune susceptibility drive region–specific disease. identified Chlamydia muridarum , an intracellular bacterium murine counterpart human sexually transmitted C....
Mitochondria oscillate along a morphological continuum from fragmented individual units to hyperfused tubular networks. Their position at the junction of catabolic and anabolic metabolism couples this plasticity, called mitochondrial dynamics, larger cellular metabolic programs, which in turn implicate mitochondria number disease states. In many cancers, engage cell with biosynthetic capacity aerobic glycolysis service proliferation progression. Chemo-resistant however, favor remodeling...
Abstract Achieving high data quality in single-cell RNA-seq (scRNA-seq) experiments has always been a significant challenge stemming from minute signal that can be detected individual cells. Droplet-based scRNA-seq additionally suffers ambient contamination, comprising nucleic acid materials released by dead cells into the loading buffer and co-encapsulated with real cells, which further washes out biological signals. Here, we developed quantitative, contamination-based metrics an associated...
Abstract Our HTAN (Human Tumor Atlas Network) study presented in Chen et al. documented single-cell RNA-sequencing (scRNA-seq) data on 128 human colonic specimens for mapping out distinct paths polyp to cancer transformations. What we have not detailed is our optimizations the droplet-based scRNA-seq approach that generate high quality from challenging tissues such as epithelium. In this work, provide a systematic dissection of tissue processing and microfluidic encapsulation factors affect...