Combining fluorescence imaging with Hi-C to study 3D genome architecture of the same single cell.
Nat Protoc
; 13(5): 1034-1061, 2018 05.
Article
en En
| MEDLINE
| ID: mdl-29674753
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.
Texto completo:
1
Colección:
01-internacional
Banco de datos:
MEDLINE
Asunto principal:
Cromatina
/
Cromosomas
/
Imagen Óptica
/
Células Madre Embrionarias de Ratones
/
Conformación Molecular
/
Biología Molecular
Límite:
Animals
Idioma:
En
Revista:
Nat Protoc
Año:
2018
Tipo del documento:
Article
País de afiliación:
Reino Unido