ArticleMethods (San Diego, Calif.)2020
Sci-Hi-C: A single-cell Hi-C method for mapping 3D genome organization in large number of single cells.
Article in Methods (San Diego, Calif.), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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Who cites it
52 citing papers in PubMed.
- Chromosome-Level Genome Assembly ofJournal of fungi (Basel, Switzerland) · 2026Article
- scCAPReSE: detection of large-scale genomic rearrangements from single-cell Hi-C based on few-shot learning.Genomics & informatics · 2026Article
- Near telomere-to-telomere genome assembly of the stone loach (Traccatichthys pulcher).Scientific data · 2026Article
- Review
- High-quality assembly of the chromosomal genome for Flemingia macrophylla reveals genomic structural characteristics.BMC genomics · 2025Article
- scHiCSRS: a self-representation smoothing method with Gaussian mixture model for imputing single cell Hi-C data.BMC bioinformatics · 2025Article
- The chromosome-scale assembly of the Salvia plebeia genome provides insight into the biosynthesis and regulation of rosmarinic acid.Plant biotechnology journal · 2025Article
- Single-Cell Hi-C Technologies and Computational Data Analysis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Review
- Mapping the 3D genome architecture.Computational and structural biotechnology journal · 2025Review
- The near-complete genome assembly ofFrontiers in plant science · 2025Article
- Chromosome-level genome assembly and annotation of the tropical sea cucumber Stichopus monotuberculatus.Scientific data · 2024Article
- ImputeHiFI: An Imputation Method for Multiplexed DNA FISH Data by Utilizing Single-Cell Hi-C and RNA FISH Data.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Epigenetic regulation of cardiovascular diseases induced by behavioral and environmental risk factors: Mechanistic, diagnostic, and therapeutic insights.FASEB bioAdvances · 2024Review
- Insights from the first chromosome-level genome assembly of the alpine gentian Gentiana straminea Maxim.DNA research : an international journal for rapid publication of reports on genes and genomes · 2024Article
- GAGE-seq concurrently profiles multiscale 3D genome organization and gene expression in single cells.Nature genetics · 2024Article
- SnapHiC-G: identifying long-range enhancer-promoter interactions from single-cell Hi-C data via a global background model.Briefings in bioinformatics · 2024Article
- Regulating epithelial-mesenchymal plasticity from 3D genome organization.Communications biology · 2024Review
- Decoding polygenic diseases: advances in noncoding variant prioritization and validation.Trends in cell biology · 2024Review
- Cepharanthine analogs mining and genomes of Stephania accelerate anti-coronavirus drug discovery.Nature communications · 2024Article
- Next-generation forward genetic screens: uniting high-throughput perturbations with single-cell analysis.Trends in genetics : TIG · 2024Review
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8 authors.
Funding
Abstract
The highly dynamic nature of chromosome conformation and three-dimensional (3D) genome organization leads to cell-to-cell variability in chromatin interactions within a cell population, even if the cells of the population appear to be functionally homogeneous. Hence, although Hi-C is a powerful tool for mapping 3D genome organization, this heterogeneity of chromosome higher order structure among individual cells limits the interpretive power of population based bulk Hi-C assays. Moreover, single-cell studies have the potential to enable the identification and characterization of rare cell populations or cell subtypes in a heterogeneous population. However, it may require surveying relatively large numbers of single cells to achieve statistically meaningful observations in single-cell studies. By applying combinatorial cellular indexing to chromosome conformation capture, we developed single-cell combinatorial indexed Hi-C (sci-Hi-C), a high throughput method that enables mapping chromatin interactomes in large number of single cells. We demonstrated the use of sci-Hi-C data to separate cells by karytoypic and cell-cycle state differences and to identify cellular variability in mammalian chromosomal conformation. Here, we provide a detailed description of method design and step-by-step working protocols for sci-Hi-C.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.