A5019436560- Single-cell and spatial transcriptomics
- Extracellular vesicles in disease
- RNA Research and Splicing
- Cell Image Analysis Techniques
- Neuroinflammation and Neurodegeneration Mechanisms
- CRISPR and Genetic Engineering
- Cancer Genomics and Diagnostics
- Molecular Biology Techniques and Applications
- Bioinformatics and Genomic Networks
- Immune cells in cancer
- Evolution and Genetic Dynamics
- CAR-T cell therapy research
- Immune Cell Function and Interaction
- Cytomegalovirus and herpesvirus research
- RNA and protein synthesis mechanisms
- Advanced Fluorescence Microscopy Techniques
- Viral Infectious Diseases and Gene Expression in Insects
- Bacteriophages and microbial interactions
- Virus-based gene therapy research
Gladstone Institutes
2023-2025
Stanford University
2023-2025
University of California, San Francisco
2024
Parker Institute for Cancer Immunotherapy
2024
Harvard University
2019-2022
The University of Texas Southwestern Medical Center
2022
Broad Institute
2019-2021
Spatial positions of cells in tissues strongly influence function, yet a high-throughput, genome-wide readout gene expression with cellular resolution is lacking. We developed Slide-seq, method for transferring RNA from tissue sections onto surface covered DNA-barcoded beads known positions, allowing the locations to be inferred by sequencing. Using we localized cell types identified single-cell sequencing datasets within cerebellum and hippocampus, characterized spatial patterns Purkinje...
High-resolution spatial transcriptomics enables mapping of RNA expression directly from intact tissue sections; however, its utility for the elucidation disease processes and therapeutically actionable pathways remains unexplored. We applied Slide-seqV2 to mouse human kidneys, in healthy distinct paradigms. First, we established feasibility nine which revealed a cell neighborhood centered around population
Abstract The precise spatial localization of molecular signals within tissues richly informs the mechanisms tissue formation and function. Previously, we developed Slide-seq, a technology which enables transcriptome-wide measurements with 10-micron resolution. Here, report new modifications to Slide-seq library generation, bead synthesis, array indexing that markedly improve mRNA capture sensitivity technology, approaching efficiency droplet-based single-cell RNAseq techniques. We...
ABSTRACT The neocortex has an unparalleled diversity of cell types, which are generated during development through a series temporally orchestrated events that under tight evolutionary constraint and critical for proper cortical assembly function. However, the molecular logic governs establishment organization types remains elusive, largely due to large number classes undergoing dynamic cell-state transitions over extended developmental timelines. Here, we have comprehensive single-cell...
ABSTRACT Tumor progression is driven by dynamic interactions between cancer cells and their surrounding microenvironment. Investigating the spatiotemporal evolution of tumors can provide crucial insights into how intrinsic changes within extrinsic alterations in microenvironment cooperate to drive different stages tumor progression. Here, we integrate high-resolution spatial transcriptomics evolving lineage tracing technologies elucidate expansion, plasticity, metastasis co-evolve with...
The widespread application of genome editing to treat or even cure disease requires the delivery editors into nucleus target cells. Enveloped Delivery Vehicles (EDVs) are engineered virally-derived particles capable packaging and delivering CRISPR-Cas9 ribonucleoproteins (RNPs). However, presence lentiviral encapsulation replication components in EDVs has obscured underlying mechanism precluded particle optimization. Here we show that Cas9 RNP nuclear is independent native capsid structure....
The widespread application of genome editing to treat and cure disease requires the delivery editors into nucleus target cells. Enveloped vehicles (EDVs) are engineered virally derived particles capable packaging delivering CRISPR-Cas9 ribonucleoproteins (RNPs). However, presence lentiviral encapsulation replication proteins in EDVs has obscured underlying mechanism precluded particle optimization. Here, we show that Cas9 RNP nuclear is independent native capsid structure. Instead,...
Abstract The spatial organization of cells in tissue has a profound influence on their function, yet high-throughput, genome-wide readout gene expression with cellular resolution is lacking. Here, we introduce Slide-seq, highly scalable method that enables facile generation large volumes unbiased transcriptomes 10 µm resolution, comparable to the size individual cells. In RNA transferred from freshly frozen sections onto surface covered DNA-barcoded beads known positions, allowing locations...
Summary Paragraph Somatic variation contributes to biological heterogeneity by modulating cellular proclivity differentiate, expand, adapt, or die. While large-scale sequencing efforts have revealed the foundational role of somatic variants drive human tumor evolution, our understanding contribution mutations modulate fitness in non-malignant contexts remains understudied. Here, we identify a mosaic synonymous variant (m.7076A>G) mitochondrial DNA (mtDNA) encoded cytochrome c-oxidase...
Abstract High resolution spatial transcriptomics is a transformative technology that enables mapping of RNA expression directly from intact tissue sections; however, its utility for the elucidation disease processes and therapeutically actionable pathways remain largely unexplored. Here we applied Slide-seqV2 to mouse human kidneys, in healthy distinct paradigms. First, established feasibility kidney by analyzing 9 donors, which revealed cell neighborhood centered around population LYVE1+...
Abstract Single-cell genomics technologies have accelerated our understanding of cell-state heterogeneity in diverse contexts. Although single-cell RNA sequencing (scRNA-seq) identifies many rare populations interest that express specific marker transcript combinations, traditional flow sorting limits ability to enrich these for further profiling, including requiring cell surface markers with high-fidelity antibodies. Additionally, studies require the isolation nuclei from tissue,...
This is a protocol detailing the steps necessary to generate libraries using previously manufactured Slide-seq arrays.