A5043737995- Cell Image Analysis Techniques
- Single-cell and spatial transcriptomics
- Neural dynamics and brain function
- Advanced Fluorescence Microscopy Techniques
- Molecular Biology Techniques and Applications
- RNA Research and Splicing
- Neuroscience and Neural Engineering
- RNA regulation and disease
- Cancer Genomics and Diagnostics
- Cell Adhesion Molecules Research
- Glioma Diagnosis and Treatment
- Neuroinflammation and Neurodegeneration Mechanisms
- CRISPR and Genetic Engineering
- Advanced Electron Microscopy Techniques and Applications
- Peptidase Inhibition and Analysis
- Advanced biosensing and bioanalysis techniques
Cold Spring Harbor Laboratory
2017-2021
An essential step toward understanding brain function is to establish a structural framework with cellular resolution on which multi-scale datasets spanning molecules, cells, circuits and systems can be integrated interpreted
Cellular DNA/RNA tags (barcodes) allow for multiplexed cell lineage tracing and neuronal projection mapping with cellular resolution. Conventional approaches to reading out barcodes trade off spatial resolution throughput. Bulk sequencing achieves high throughput but sacrifices resolution, whereas manual picking has low In situ could potentially achieve both throughput, current in techniques are inefficient at barcodes. Here we describe BaristaSeq, an optimization of a targeted, padlock...
Abstract An essential step toward understanding brain function is to establish a cellular-resolution structural framework upon which multi-scale and multi-modal information spanning molecules, cells, circuits systems can be integrated interpreted. Here, through collaborative effort from the Brain Initiative Cell Census Network (BICCN), we derive comprehensive cell type-based description of one structure - primary motor cortex upper limb area (MOp-ul) mouse. Applying state-of-the-art...
The function of a neural circuit is determined by the details its synaptic connections. At present, only available method for determining wiring diagram with single synapse precision-a 'connectome'-is based on imaging methods that are slow, labor-intensive and expensive. Here, we present SYNseq, converting connectome into form can exploit speed low cost modern high-throughput DNA sequencing. In each neuron labeled unique random nucleotide sequence-an RNA 'barcode'-which targeted to using...
Summary Understanding neural circuits requires deciphering interactions among myriad cell types defined by spatial organization, connectivity, gene expression, and other properties. Resolving these both single neuron resolution high throughput, a challenging combination with conventional methods. Here we introduce BARseq, multiplexed method based on RNA barcoding for mapping projections of thousands spatially resolved neurons in brain, relating those to properties such as or Cre expression....
Abstract Functional circuits consist of neurons with diverse axonal projections and gene expression. Understanding the molecular signature requires high-throughput interrogation both expression to multiple targets in same cells at cellular resolution, which is difficult achieve using current technology. Here, we introduce BARseq2, a technique that simultaneously maps detects multiplexed by situ sequencing. We determined cadherins cell-type markers 29,933 cells, 3,164 mouse motor cortex...
Abstract Cellular DNA/RNA tags (barcodes) allow for multiplexed cell lineage tracing and neuronal projection mapping with cellular resolution. Conventional approaches to reading out barcodes trade off spatial resolution throughput. Bulk sequencing achieves high throughput but sacrifices resolution, whereas manual picking has low In situ could potentially achieve both throughput, current in techniques are inefficient at barcodes. Here we describe BaristaSeq, an optimization of a targeted,...
Abstract The function of a neural circuit is determined by the details its synaptic connections. At present, only available method for determining wiring diagram with single synapse precision—a “connectome”—is based on imaging methods that are slow, labor-intensive and expensive. Here we present SYNseq, converting connectome into form can exploit speed low cost modern high-throughput DNA sequencing. In each neuron labeled unique random nucleotide sequence—an RNA “barcode”—which targeted to...
This protocol describes the in situ sequencing steps of BARseq, a high-throughput axonal projection mapping technique based on cellular RNA barcoding. In brain area interest is infected with Sindbis barcoded library. After 24-48 hrs, injection site punched out, frozen, and processed using this protocol. Other potential target sites are dissected sequenced as described by Kebschull et al.., 2016. Proejctions then determined for cells matching their barcodes (sequenced protocol) to at sites.