A5003620840- Single-cell and spatial transcriptomics
- Cell Image Analysis Techniques
- Advanced Fluorescence Microscopy Techniques
- CRISPR and Genetic Engineering
- Genomics and Chromatin Dynamics
- Advanced Biosensing Techniques and Applications
- RNA Research and Splicing
- Image Processing Techniques and Applications
- Pluripotent Stem Cells Research
- 3D Printing in Biomedical Research
- Spaceflight effects on biology
- Advanced biosensing and bioanalysis techniques
- Liver physiology and pathology
- Neuroinflammation and Neurodegeneration Mechanisms
- Molecular Biology Techniques and Applications
- Advanced Electron Microscopy Techniques and Applications
- Liver Diseases and Immunity
- Polysaccharides and Plant Cell Walls
- RNA and protein synthesis mechanisms
- Plant Reproductive Biology
- Neuroscience and Neural Engineering
- Plant Molecular Biology Research
- Liver Disease and Transplantation
California Institute of Technology
2012-2018
Stanford University
2018
Hampshire College
2011
University of Massachusetts Amherst
2011
Accurate and robust detection of mRNA molecules in thick tissue samples can reveal gene expression patterns single cells within their native environment. Preserving spatial relationships while accessing the transcriptome selected is a crucial feature for advancing many biological areas - from developmental biology to neuroscience. However, because high autofluorescence background samples, it difficult detect single-molecule fluorescence situ hybridization (smFISH) signals robustly opaque...
We have used propidium iodide (PI) to investigate the dynamic properties of primary cell wall at apex Arabidopsis (Arabidopsis thaliana) root hairs and pollen tubes in lily (Lilium formosanum) tubes. Our results show that hairs, as tubes, oscillatory peaks PI fluorescence precede growth rate oscillations. Pectin forms component tip both Given electronic structure PI, we investigated whether binds pectins a manner analogous Ca(2+) binding. first is able abrogate inhibition dose-dependent...
Abstract Pooled CRISPR screening has emerged as a powerful method of mapping gene functions thanks to its scalability, affordability, and robustness against well or plate-specific confounders present in array-based 1–6 . Most pooled screens assay for low dimensional phenotypes (e.g. fitness, fluorescent markers). Higher-dimensional assays such perturb-seq are available but costly only applicable transcriptomics readouts 7–11 Recently, optical screening, which combines microscopy-based...
ABSTRACT Optical pooled screening (OPS) is a highly scalable method for linking image-based phenotypes with cellular perturbations. However, it has thus far been restricted to relatively low-plex phenotypic readouts in cancer cell lines culture, due limitations associated situ sequencing (ISS) of perturbation barcodes. Here, we developed PerturbView, an OPS technology that leverages vitro transcription (IVT) amplify barcodes prior ISS, enabling screens multiplexed across diverse systems,...
Summary Recent single cell experiments have revealed significant heterogeneities at the levels of transcription, DNA methylation and chromosome organization in individual cells. However, existing method profiling mRNAs effectively averages transcriptional dynamics over many hours due to hours-long life time most mRNAs. To capture instantaneous activity transcriptome that reflects rapid regulatory changes cells, we imaged up 10,421 nascent transcription active sites (TAS) mouse embryonic stem...
Visualization of the transcriptome and nuclear organization in situ individual cell is holy grail single analysis. Here, we demonstrate a multiplexed molecule method, intron seqFISH, that allows imaging 10,421 genes at their nascent transcription active sites cells, followed by mRNA lncRNA seqFISH immunofluorescence. This profiling method can identify different types states with mouse embryonic stem cells fibroblasts. The RNA synthesis tend to be localized on surfaces chromosome territories...