Single Nucleus
Single Nucleus - Related Videos
11:52
Analysis of LINE-1 Retrotransposition at the Single Nucleus Level
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2016
Here we employ FISH methodology to track LINE-1 retrotransposition at the single nuclei level in chromosome spreads of HepG2 cell lines stably expressing synthetic LINE-1.
03:42
Rapid Dissection and Dissociation of the Mouse Olfactory Epithelium for Single-Nucleus Suspensions
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Cited by 1 •
2025
This article provides a streamlined protocol for the dissection and dissociation of murine olfactory epithelium for the purpose of single-nucleus RNA sequencing.
06:38
Isolation of Adult Spinal Cord Nuclei for Massively Parallel Single-nucleus RNA Sequencing
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Cited by 69 •
2018
Here, we present a protocol to rapidly isolate high-quality nuclei from the fresh or frozen tissue for downstream massively parallel RNA sequencing. We include detergent-mechanical and hypotonic-mechanical tissue disruption and cell lysis options, both of which can be used for isolation of nuclei.
05:13
Co-culturing of Ventral Hippocampal and Nucleus Accumbens
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2025
This video demonstrates the process of preparing ventral hippocampal and nucleus accumbens tissues from mouse brains for co-culture. Neurons extend projections to form synaptic connections between the ventral hippocampal and nucleus accumbens tissues. This method allows studying neuronal interactions between these two brain regions, offering insights into cognition, behavior, and neurological disorders.
06:08
Preparation and Immunofluorescence Staining of Bundles and Single Fiber Cells from the Cortex and Nucleus of the Eye Lens
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Cited by 7 •
2023
This protocol describes methods to prepare peripheral, mature, and nuclear eye lens fiber cells for immunofluorescence staining to study complex cell-to-cell interdigitations and the membrane architecture.
FAQs
The key advantage is that nuclei can be recovered when intact-cell dissociation is difficult or damaging. This makes the approach useful for fragile tumors and tissues whose architecture or cellular material is not readily preserved during preparation. By retaining access to nuclear RNA, DNA, or chromatin, researchers can examine molecular variation that might otherwise be missed in whole-tissue measurements.
Different nuclear readouts answer different biological questions. Nuclear RNA profiling describes transcriptional states, DNA measurements support genetic characterization, and chromatin measurements examine epigenetic features. Selecting the appropriate signal allows researchers to focus on how genes are expressed, how genetic features vary, or how epigenetic organization differs among tumor and surrounding cell populations.
Compared with approaches that require intact-cell dissociation, Single Nucleus methods are suited to samples in which that preparation is challenging. Their value is especially apparent for fragile tumors and complex tissue architecture, where recovering nuclei can support molecular profiling even when intact cells are difficult to obtain. This expands the range of cancer specimens available for analysis.
Measuring individual nuclei enables researchers to distinguish molecularly different cell states within the same tumor. Instead of treating the specimen as a uniform population, investigators can identify variation among groups of nuclei and relate those differences to tumor progression or treatment response. This resolution is important for understanding why genetically or transcriptionally diverse regions may coexist within one cancer.
Single Nucleus workflows can begin with fresh, frozen, or archived samples. After nuclei are isolated, sequencing-based assays measure nuclear RNA, DNA, or chromatin. This sample flexibility allows researchers to investigate material that may not be suitable for intact-cell analysis, while the selected molecular readout determines whether the study emphasizes transcriptional, genetic, or epigenetic features.
Profiling individual nuclei can resolve tumor and stromal cell populations within the same cancer specimen. That separation lets researchers compare molecular features across populations instead of interpreting the tissue as a single undifferentiated signal. In practice, this supports more precise analysis of which cell populations carry states associated with progression or treatment response.
Because it captures molecular differences among nuclei and populations within a tumor, the method can expose patterns linked to cancer evolution. Researchers can use those patterns to examine how diverse cell states are distributed across a specimen and identify molecular changes that may represent therapeutic targets. This connects cellular heterogeneity with questions about progression and treatment response.