Single Nucleus Atac-seq
Single Nucleus Atac-seq - Related Videos
06:22
Nuclei Isolation from Fresh Frozen Brain Tumors for Single-Nucleus RNA-seq and ATAC-seq
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Cited by 15 •
2020
Intra-tumoral heterogeneity is an inherent feature of tumors, including gliomas. We developed a simple and efficient protocol that utilizes a combination of buffers and gradient centrifugation to isolate single nuclei from fresh frozen glioma tissues for single nucleus RNA and ATAC sequencing studies.
11:11
Adipocyte-Specific ATAC-Seq with Adipose Tissues Using Fluorescence-Activated Nucleus Sorting
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Cited by 2 •
2023
We present a protocol for assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) specifically on adipocytes using nucleus sorting with adipose tissues isolated from transgenic reporter mice with nuclear fluorescence labeling.
07:13
ATAC-Seq Optimization for Cancer Epigenetics Research
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Cited by 6 •
2022
ATAC-seq is a DNA sequencing method that uses the hyperactive mutant transposase, Tn5, to map changes in chromatin accessibility mediated by transcription factors. ATAC-seq enables the discovery of the molecular mechanisms underlying phenotypic alterations in cancer cells. This protocol outlines optimization procedures for ATAC-seq in epithelial cell types, including cancer cells.
09:44
ATAC-Seq Library Preparation of Murine Bone Marrow-Derived Neutrophils
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Cited by 2 •
2025
This manuscript outlines a protocol for preparing an ATAC-seq library of neutrophils from murine bone marrow, aiming to guarantee optimal neutrophil viability and high library quality. It offers step-by-step instructions on BMC preparation, immunomagnetic sorting, and library construction, serving as a valuable guide, especially for newcomers to studying neutrophils.
09:54
RNA-Seq
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2023
Among different methods to evaluate gene expression, the high-throughput sequencing of RNA, or RNA-seq. is particularly attractive, as it can be performed and analyzed without relying on prior available genomic information. During RNA-seq, RNA isolated from samples of interest is used to generate a DNA library, which is then amplified and sequenced. Ultimately, RNA-seq can determine which genes are expressed, the levels of their expression, and the presence of any previously unknown transcripts.
FAQs
During library preparation, the transposase inserts sequencing adapters preferentially at accessible chromatin. This makes open regulatory DNA recoverable in sequence libraries, so read patterns can identify promoters, enhancers, and other regulatory elements. Because accessibility differs among nuclei, the resulting profiles help connect regulatory state with cell identity and cancer-related transcriptional programs.
Single-nucleus resolution preserves differences that could be obscured when tumor material is considered as one population. The resulting profiles can separate malignant, immune, and stromal populations and show how regulatory states vary across them. In cancer research, this supports analysis of heterogeneous tumors and links epigenetic changes to distinct cellular programs.
Accessible promoters and enhancers provide complementary regulatory information. Promoters and enhancers represent regulatory elements whose accessibility can vary between cell populations. Examining both, along with other accessible regions, helps relate cell identity to transcriptional programs and identify epigenetic differences within a tumor.
The workflow proceeds from nuclei isolation to transposase treatment, followed by sequencing of the DNA fragments carrying inserted adapters. Sequence information is then used to locate accessible genomic regions, including promoters, enhancers, and other regulatory elements. Keeping these stages conceptually distinct clarifies how physical chromatin state becomes a cell-resolved genomic profile.
Nuclei-based profiling can be useful when tissues are archived or difficult to dissociate. Rather than requiring readily separated whole cells, the approach works with isolated nuclei, allowing regulatory states to be examined in challenging tumor material. This expands access to heterogeneous cancer specimens and supports comparison of distinct cellular populations.
By comparing accessibility patterns across nuclei and cell populations, researchers can connect regulatory states with tumor cell identity and transcriptional programs. In cancer research, those relationships help investigate tumor evolution and reveal potential therapeutic vulnerabilities. The same data also distinguish malignant, immune, and stromal populations, providing cellular context for interpreting epigenetic changes within heterogeneous tumors.