Chromatin-bound protein colocalization analysis using bedGraph2Cluster and PanChIP.
STAR Protoc
; 4(1): 101991, 2023 03 17.
Article
en En
| MEDLINE
| ID: mdl-36607812
ABSTRACT
Computational pipelines for chromatin immunoprecipitation sequencing analysis can neglect colocalization events that occur in a mere subset of the genome. Here, we detail a streamlined approach for assessing colocalization of chromatin-bound proteins using the bedGraph2Cluster and PanChIP algorithms. Using histone modifications as an example, bedGraph2Cluster performs clustering analysis on chromatin binding patterns of target proteins. PanChIP then compares these clusters with a reference library of chromatin binding patterns and measures the overlap in peaks, capturing the heterogeneity in chromatin binding and colocalization patterns. For complete details on the use and execution of this protocol, please refer to Sanidas et al. (2022).1.
Palabras clave
Texto completo:
1
Colección:
01-internacional
Banco de datos:
MEDLINE
Asunto principal:
Cromatina
/
Secuenciación de Nucleótidos de Alto Rendimiento
Idioma:
En
Revista:
STAR Protoc
Año:
2023
Tipo del documento:
Article