ArticleNature protocols2018
Combining fluorescence imaging with Hi-C to study 3D genome architecture of the same single cell.
Article in Nature protocols, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
10 citing papers in PubMed, 16 citations in OpenAlex.
- Dynamic changes in 3D chromatin structure during male gametogenesis in Arabidopsis thaliana.Genome biology · 2025Article
- Enhancer-promoter interactions are reconfigured through the formation of long-range multiway hubs as mouse ES cells exit pluripotency.Molecular cell · 2024Article
- Live-cell three-dimensional single-molecule tracking reveals modulation of enhancer dynamics by NuRD.Nature structural & molecular biology · 2023Article
- Enhancer-Promoter Communication: It's Not Just About Contact.Frontiers in molecular biosciences · 2022Article
- Studying the Dynamics of Chromatin-Binding Proteins in Mammalian Cells Using Single-Molecule Localization Microscopy.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Single-cell Hi-C data analysis: safety in numbers.Briefings in bioinformatics · 2021Article
- FISH Going Meso-Scale: A Microscopic Search for Chromatin Domains.Frontiers in cell and developmental biology · 2021Review
- Enrichment of rare events using a multi-parameter high throughput microfluidic droplet sorter.Lab on a chip · 2020Article
- Towards mapping the 3D genome through high speed single-molecule tracking of functional transcription factors in single living cells.Methods (San Diego, Calif.) · 2020Article
- Calculation of 3D genome structures for comparison of chromosome conformation capture experiments with microscopy: An evaluation of single-cell Hi-C protocols.Nucleus (Austin, Tex.) · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
13 authors at 3 institutions in 1 country.
Funding
Abstract
Fluorescence imaging and chromosome conformation capture assays such as Hi-C are key tools for studying genome organization. However, traditionally, they have been carried out independently, making integration of the two types of data difficult to perform. By trapping individual cell nuclei inside a well of a 384-well glass-bottom plate with an agarose pad, we have established a protocol that allows both fluorescence imaging and Hi-C processing to be carried out on the same single cell. The protocol identifies 30,000-100,000 chromosome contacts per single haploid genome in parallel with fluorescence images. Contacts can be used to calculate intact genome structures to better than 100-kb resolution, which can then be directly compared with the images. Preparation of 20 single-cell Hi-C libraries using this protocol takes 5 d of bench work by researchers experienced in molecular biology techniques. Image acquisition and analysis require basic understanding of fluorescence microscopy, and some bioinformatics knowledge is required to run the sequence-processing tools described here.
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Registered trials
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.