A5009819780- Molecular Biology Techniques and Applications
- RNA Research and Splicing
- Single-cell and spatial transcriptomics
- Advanced biosensing and bioanalysis techniques
- RNA and protein synthesis mechanisms
- Advanced Fluorescence Microscopy Techniques
- Cell Image Analysis Techniques
- RNA modifications and cancer
- 3D Printing in Biomedical Research
- Mitochondrial Function and Pathology
- Neuroscience and Neural Engineering
- Genomics and Phylogenetic Studies
- Neural dynamics and brain function
- Various Chemistry Research Topics
- CRISPR and Genetic Engineering
- Genomics and Chromatin Dynamics
- Genetic Neurodegenerative Diseases
Harvard University
2013-2021
Center for Systems Biology
2013-2020
ReadCoor (United States)
2020
Inspire
2020
Massachusetts Institute of Technology
2018
University of Pennsylvania
2012
Transcripts Visualized in Situ Despite advances, current methods for single-cell sequencing are unable to resolve transcript location within the cell, so Lee et al. (p. 1360 , published online 27 February) developed a method of fluorescent situ RNA (FISSEQ) that works vivo show messenger localization cells. The amplifies complementary DNA targets by rolling circle amplification, and then cross-linking locks amplicons produce ample, highly localized templates three-dimensional sequencing....
Identifying transcript location in cells where specific RNAs occur within a cell or tissue has been limited by technology and imaging capabilities. Expansion microscopy allowed for better visualization of small structures expanding the tissues with polymer- hydrogel-based system. Alon et al. combined expansion long-read situ RNA sequencing, resulting more precise transcripts. This method, termed “ExSeq” was used to detect RNAs, both new transcripts those previously demonstrated localize...
Abstract: Methods for highly multiplexed RNA imaging are limited in spatial resolution, and thus their ability to localize transcripts nanoscale subcellular compartments. We adapt expansion microscopy, which physically expands biological specimens, long-read untargeted targeted situ sequencing. applied sequencing (ExSeq) mouse brain, yielding readout of thousands genes, including splice variants novel transcripts. Targeted ExSeq yielded nanoscale-resolution maps RNAs throughout dendrites...
Antisense transcription, or transcription on the opposite strand of same genomic locus as another transcript, has been observed in many organisms, including yeast. Several antisense transcripts are known to be conserved across various species yeast, and a few associated with functional regulation sense transcript. We detect from approximately 90% protein-coding genes, is generally histone modifications indicative transcriptionally active state. The pattern genome-wide two budding...
We propose a neural connectomics strategy called Fluorescent In-Situ Sequencing of Barcoded Individual Neuronal Connections (FISSEQ-BOINC), leveraging fluorescent in situ nucleic acid sequencing fixed tissue (FISSEQ). FISSEQ-BOINC exhibits different properties from BOINC, which relies on bulk sequencing. could become scalable approach for mapping whole-mammalian-brain connectomes with rich molecular annotations.
Abstract We analyze the scaling and cost-performance characteristics of current projected connectomics approaches, with reference to potential implications recent advances in diverse contributing fields. Three generalized strategies for dense connectivity mapping at scale whole mammalian brains are considered: electron microscopic axon tracing, optical imaging combinatorial molecular markers synapses, bulk DNA sequencing trans-synaptically exchanged nucleic acid barcode pairs. Due...
Fluorescent spatial sequencing brings next-generation into a new realm capable of identifying nucleic acids in the cell's natural environment. For first time, scientists are able to multiplex assignment specific locations hundreds transcriptional targets and lay foundation for understanding how genetic changes control fate each cell within tissue microenvironment. In this perspective, we discuss capabilities fluorescent context other imaging technologies describe these offer data-rich,...
These are Expansion FISH (ExFISH) protocols forsuper-resolution imaging of RNA structure and location with diffraction-limited microscopes. Please select the appropriate protocol depending on your sample (cells or tissue).
The ability to image RNA identity and location with nanoscale precision in intact tissues is of great interest for defining cell types states normal pathological biological settings. Here, we present a strategy expansion microscopy RNA. We developed small-molecule linker that enables be covalently attached swellable polyelectrolyte gel synthesized throughout specimen. Then, postexpansion, fluorescentin situhybridization (FISH) imaging can performed high yield specificity as well...
The ability to image RNA identity and location with nanoscale precision in intact tissues is of great interest for defining cell types states normal pathological biological settings. Here, we present a strategy expansion microscopy RNA. We developed small-molecule linker that enables be covalently attached swellable polyelectrolyte gel synthesized throughout specimen. Then, postexpansion, fluorescentin situhybridization (FISH) imaging can performed high yield specificity as well...
RNA sequencing measures the quantitative change in gene expression over whole transcriptome, but it lacks spatial context. On other hand, situ hybridization provides location of expression, only for a small number genes. Here we detail protocol genome-wide profiling fixed cells and tissues, which is converted into cross-linked cDNA amplicons sequenced manually on confocal microscope. Unlike traditional RNA-seq our method enriches context-specific transcripts house-keeping and/or structural...
The ability to image RNA identity and location with nanoscale precision in intact tissues is of great interest for defining cell types states normal pathological biological settings. Here, we present a strategy expansion microscopy RNA. We developed small-molecule linker that enables be covalently attached swellable polyelectrolyte gel synthesized throughout specimen. Then, postexpansion, fluorescentin situhybridization (FISH) imaging can performed high yield specificity as well...