Nuclei Permeabilization
Nuclei Permeabilization - Related Videos
04:43
A Technique to Isolate Nuclei from Non-neuronal Cells in the Hippocampal Dentate Gyrus
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2025
The video demonstrates a method for isolating intact nuclei from glial and stem cells in the mouse hippocampal dentate gyrus (DG). The DG tissue is mechanically dissociated in a cold homogenization buffer to release the nuclei. Tissue debris and other released organelles are discarded, and the nuclei are stained with a DNA stain and a fluorophore-conjugated antibody specific for the neuronal nuclear antigen (NeuN). Fluorescence-activated nuclei sorting is then employed to isolate the...
03:05
Gradient Centrifugation Based Purification of Nuclei: A Technique to Obtain Ultrapure Fraction of Intact Nuclei Using Density Gradient Centrifugation
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2023
In this video, we describe a simple and efficient protocol using gradient centrifugation to isolate single nuclei. Once isolated, these nuclei can be used for sequencing and genome analysis.
05:59
Isolation of Nuclei from Human Intermuscular Adipose Tissue and Downstream Single-Nuclei RNA Sequencing
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Cited by 2 •
2024
The biology of intermuscular adipose tissue (IMAT) is largely unexplored due to the limited accessibility of human tissue. Here, we present a detailed protocol for nuclei isolation and library preparation of frozen human IMAT for single nuclei RNA sequencing to identify the cellular composition of this unique adipose depot.
03:55
Isolation of Nuclei from Fresh Frozen Glioma Tissues: A Method to Obtain Intact Nuclei from Glioma Tumor Samples
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2023
This video describes the protocol to isolate single-nuclei from fresh frozen glioma tissue. The isolated single-nuclei can be used as specimens for sequencing techniques such as single-nuclei RNA (snRNA) sequencing and single-nuclei Assay for Transposase-Accessible Chromatin (snATAC) sequencing to obtain deeper insights into inter- and intra-tumor heterogeneity observed in glioma of the central nervous tissues.
06:25
Using Computer Vision Libraries to Streamline Nuclei Quantification
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Cited by 1 •
2025
This article describes step-by-step methods to automate image-based nuclei quantification using an open-source executable program validated across a range of cell densities. This program provides an alternative that addresses barriers related to cost, accessibility for users with limited technological skillsets, and application-specific validation that may limit utility of existing technologies.
FAQs
Outcome depends on how strongly the nuclear envelope is opened and how well treatment preserves nuclear contents. Chemical detergents, enzymatic treatment, and related conditions provide different ways to create temporary or selective access. Researchers therefore adjust treatment parameters to improve molecular entry without compromising chromatin, DNA, or overall nuclear structure, which determines the quality of downstream genetic measurements.
Controlled access matters because nuclear entry alone is not the goal; the contents must remain sufficiently intact for interpretation. Excessive modification can damage structural or genetic contents, whereas insufficient access can limit delivery of antibodies, probes, or enzymes. The useful operating range is therefore a balance between permeability and preservation, especially when examining chromatin organization or DNA-associated proteins.
Unlike approaches that merely expose material outside the nucleus, Nuclei Permeabilization is designed to improve access within the nuclear compartment. Its selectivity can be tuned through chemical, enzymatic, or related treatment conditions, while fixation helps constrain damage. This distinction is important when signals must be assigned to chromatin, DNA, or nuclear architecture rather than to surrounding cellular material.
A practical workflow pairs fixation with a carefully selected permeabilization treatment, then introduces the molecule or reagent required for the assay. The relevant variables are the fixation and treatment parameters, which must be adjusted to preserve nuclear structure while allowing access. This sequence supports later fluorescence staining, in situ hybridization, immunolabeling, or enzyme-based analysis.
The choice of probe, antibody, enzyme, or other molecule should match the nuclear target and intended readout. Probes can support DNA-related localization, antibodies can reveal nuclear or DNA-associated proteins, and enzymes can support enzyme-based assays. Improved entry makes these reagents more useful for studying genome organization, gene regulation, and chromatin-associated features.
In genetics, the method is valuable when researchers need molecular signals from inside preserved nuclei rather than information from bulk cellular material. Applications include fluorescence staining, in situ hybridization, immunolabeling, and enzyme-based assays. These approaches can provide insight into genome organization, gene regulation, DNA-associated proteins, and nuclear architecture, depending on the reagent and assay used.