Nuclei Extraction
Nuclei Extraction - Related Videos
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.
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.
10:58
Neuronal Nuclei Isolation from Human Postmortem Brain Tissue
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Cited by 136 •
2008
The cellular heterogeneity of brain tissue poses a significant limitation for the study of epigenetic markings in chromatin because most assays lack single cell resolution. Neurons typically are intermingled with glia and other non-neuronal cells. We provide a protocol to extract and collect neuronal nuclei from human brain.
02:43
Isolation of Oxytocin Receptor-Rich Nuclei from a Neonatal Rat Brain
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2025
This video demonstrates the isolation of oxytocin receptor-rich nuclei from the neonatal rat brain. Coronal slicing, followed by identification and precise punching of oxytocin receptor-rich brain nuclei, enables the effective extraction of oxytocin receptor-rich nuclei for further analysis.
10:12
Isolation of Cardiomyocyte Nuclei from Post-mortem Tissue
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Cited by 61 •
2012
Cardiac nuclei are isolated via density sedimentation and immunolabeled with antibodies against pericentriolar material 1 (PCM-1) to identify and sort cardiomyocyte nuclei by flow cytometry.
FAQs
These steps separate the objectives of releasing nuclei and preserving them. Mechanical disruption breaks apart intact cells or tissue, while selective lysis targets the plasma membrane so nuclear structures remain available for recovery. Balancing both actions helps retain information about cell identity and state, which is essential when extracted nuclei will be analyzed for molecular differences.
Filtration removes larger tissue fragments and other incompletely disrupted material before centrifugation. Centrifugation then separates nuclei from remaining cytoplasmic components according to their physical behavior during spinning. Together, these stages produce a preparation enriched for nuclei rather than a mixture dominated by cellular debris, supporting more focused analysis of nuclear DNA, RNA, or chromatin.
The extraction conditions must limit two competing problems: nuclear damage and aggregation. Excessive disruption can compromise nuclear integrity, whereas insufficiently controlled handling can leave nuclei clustered together. Adjusting the conditions to the starting cells or tissue helps maintain separable nuclei and preserves interpretable information about nuclear material and cellular state.
A typical workflow begins with mechanical disruption of intact cells or tissue, followed by selective lysis of the plasma membrane. The resulting material is filtered to remove unsuitable fragments and then centrifuged to separate nuclei from cytoplasmic components. Conditions are adjusted throughout the process to reduce damage and aggregation before the isolated nuclei are analyzed.
Nuclei extraction supports measurements of chromatin accessibility, nuclear RNA, DNA content, and gene regulation. These readouts allow investigators to examine how nuclear states differ among changing cell populations. In developmental biology, that information can connect molecular regulation with tissue formation and differentiation, where cell identity and regulatory programs change over time.
Nuclei extraction can provide access to nuclear information even when intact cells are difficult to recover cleanly from a sample. This makes the approach useful for archived or fragile tissues, as well as materials that resist dissociation. The resulting nuclear profiles can help characterize cell populations and regulatory changes during developmental processes.