Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Chromatin Immunoprecipitation- ChIP02:36

Chromatin Immunoprecipitation- ChIP

11.2K
Chromatin immunoprecipitation, or ChIP, is an antibody-based technique used to identify sites on DNA that bind to transcription factors of interest or histone proteins. It also helps determine the type of histone modifications such as acetylation, phosphorylation, or methylation.
Types of ChIP
ChIP can be divided into two types - X-ChIP and N-ChIP. X-ChIP involves in vivo cross-linking of histones and regulatory proteins to DNA, fragmenting the DNA by sonication, and isolating the protein-DNA...
11.2K
Heterochromatin02:38

Heterochromatin

14.1K
The extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions that take up more dye are called heterochromatin. Heterochromatin is further classified into two forms – constitutive heterochromatin and facultative heterochromatin.
Constitutive heterochromatin: It is a highly compact region of chromatin that is mostly concentrated in the centromere and telomere. Unlike euchromatin, the amino acid at...
14.1K
Chromatin Packaging01:32

Chromatin Packaging

16.8K
Each human somatic cell contains 6 billion base pairs of DNA. Each base pair is 0.34 nm long, meaning each diploid cell contains a staggering 2 meters of DNA. This long DNA strand is packed inside a nucleus measuring only 10-20 microns in diameter with the help of specialized DNA-binding proteins called histones. Together they form a compact DNA-protein complex called chromatin. The chromatin is further compacted into higher-order structures. The highest level of compaction is achieved during...
16.8K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Early postnatal DNA methylation dynamics define neuronal subtypes and are disrupted by MECP2 loss.

bioRxiv : the preprint server for biology·2026
Same author

Mutant ASXL1 Drives Transcriptional Activation and Repression in Human Hematopoiesis.

bioRxiv : the preprint server for biology·2026
Same author

Single-cell DNA methylation analysis tool Amethyst resolves distinct non-CG methylation patterns in human astrocytes and oligodendrocytes.

Communications biology·2025
Same author

The Prolyl Isomerase PIN1 Affects Fibroblast Differentiation States and Cross-talk in Pancreatic Cancer.

Cancer research·2025
Same author

Ongoing replication stress tolerance and clonal T cell responses distinguish liver and lung recurrence and outcomes in pancreatic cancer.

Nature cancer·2025
Same author

Atlas-scale single-cell DNA methylation profiling with sciMETv3.

Cell genomics·2024
Same journal

Complete sequencing of medaka genomes reveals the architecture of centromeric satellites, giant mobile elements, and sex chromosomes.

Genome research·2026
Same journal

Convergence and conflict among telomere specialized transposons across 60 million years of Drosophilid evolution.

Genome research·2026
Same journal

A unified analysis of cell type- and trajectory-associated pathways in single-cell data using Phoenix.

Genome research·2026
Same journal

Resf1 is required for proper placental development and configuration of trophoblast cell-specific heterochromatin.

Genome research·2026
Same journal

Telomere-driven replicative crisis is driven by large-scale changes in genomic architecture.

Genome research·2026
Same journal

Spatially informed reference-free cell-type deconvolution for spatial transcriptomics with SpatialCD.

Genome research·2026
See all related articles

Related Experiment Video

Updated: Aug 9, 2025

Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq
09:08

Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq

Published on: November 13, 2017

18.1K

Atlas-scale single-cell chromatin accessibility using nanowell-based combinatorial indexing.

Brendan L O'Connell1, Ruth V Nichols1, Dmitry Pokholok2

  • 1Oregon Health & Science University, Department of Molecular and Medical Genetics, Portland, Oregon 97239, USA.

Genome Research
|February 15, 2023
PubMed
Summary
This summary is machine-generated.

We developed a cost-effective nanowell chip for single-cell combinatorial indexed Assay for Transposase Accessible Chromatin (sciATAC), enabling large-scale chromatin accessibility profiling of over 100,000 cells. This advancement significantly reduces costs while maintaining high data quality.

More Related Videos

Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis
10:05

Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis

Published on: December 12, 2017

22.3K
Single-Cell Factor Localization on Chromatin using Ultra-Low Input Cleavage Under Targets and Release using Nuclease
09:20

Single-Cell Factor Localization on Chromatin using Ultra-Low Input Cleavage Under Targets and Release using Nuclease

Published on: February 1, 2022

2.8K

Related Experiment Videos

Last Updated: Aug 9, 2025

Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq
09:08

Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq

Published on: November 13, 2017

18.1K
Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis
10:05

Generation of Native Chromatin Immunoprecipitation Sequencing Libraries for Nucleosome Density Analysis

Published on: December 12, 2017

22.3K
Single-Cell Factor Localization on Chromatin using Ultra-Low Input Cleavage Under Targets and Release using Nuclease
09:20

Single-Cell Factor Localization on Chromatin using Ultra-Low Input Cleavage Under Targets and Release using Nuclease

Published on: February 1, 2022

2.8K

Area of Science:

  • Genomics
  • Epigenomics
  • Cell Biology

Background:

  • Measuring chromatin accessibility at single-cell resolution is crucial for understanding cell type heterogeneity.
  • Existing single-cell Assay for Transposase Accessible Chromatin (scATAC) methods face limitations in throughput and cost.
  • Scaling up single-cell epigenomic profiling is essential for creating comprehensive cellular atlases.

Purpose of the Study:

  • To present advancements in single-cell combinatorial indexed Assay for Transposase Accessible Chromatin (sciATAC) using nanowell chips.
  • To achieve atlas-scale cell throughput (>10^5 cells) at a reduced cost.
  • To enable high-resolution mapping of cell types and subtypes in complex tissues.

Main Methods:

  • Leveraging nanowell chips for polymerase chain reaction (PCR)-based indexing in sciATAC.
  • Implementing three workflow variants to balance cell throughput and data depth.
  • Applying the optimized methods to banked mouse brain tissue for epigenomic profiling.

Main Results:

  • Achieved a 52-fold improvement in scale and reduced per-cell preparation costs compared to previous methods.
  • Demonstrated high fraction of reads within called peaks (>80%) and low cell doublet rates.
  • Successfully mapped cell types and neuronal subtypes, integrating with existing scATAC and scRNA-seq data.

Conclusions:

  • The developed nanowell-based sciATAC platform offers a scalable and cost-effective solution for single-cell epigenomics.
  • The method provides high-quality chromatin accessibility data with minimal cell-to-cell cross-talk.
  • This advancement facilitates the creation of large-scale cellular atlases and deepens our understanding of cell-type-specific regulatory landscapes.