Genomics

Dataset Information

199

HiChIP: Efficient and sensitive analysis of protein-directed genome architecture


ABSTRACT: Three-dimensional genome structure is central to gene control, but current technologies are often impractical for many biological questions due to cell and read number requirements. Here we present HiChIP, a protein-centric chromatin conformation method. HiChIP improves the fraction of conformation-informative reads by over 10-fold and lowers input requirement greater than 100-fold to 1 million cells. HiChIP of cohesin reveals multi-scale genome architecture with greater signal to noise than in situ Hi-C. Thus, HiChIP will enable insight into the genome’s three-dimensional structure and regulation in once-inaccessible biological systems. Overall design: [HiChIP cohesin] GM and mESC 25m (25 million cell input): 2 biological with 2 technical replicates, mESC 10m, 5m, and 1m: 2 technical replicates [HiChIP oct4] mESC 25m (25 million cell input): 2 biological with 2 technical replicates

INSTRUMENT(S): Illumina HiSeq 4000 (Homo sapiens)

SUBMITTER: Ryan Alexander Flynn  

PROVIDER: GSE80820 | GEO | 2016-08-31

SECONDARY ACCESSION(S): PRJNA320090

REPOSITORIES: GEO

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HiChIP: efficient and sensitive analysis of protein-directed genome architecture.

Mumbach Maxwell R MR   Rubin Adam J AJ   Flynn Ryan A RA   Dai Chao C   Khavari Paul A PA   Greenleaf William J WJ   Chang Howard Y HY  

Nature methods 20160919 11


Genome conformation is central to gene control but challenging to interrogate. Here we present HiChIP, a protein-centric chromatin conformation method. HiChIP improves the yield of conformation-informative reads by over 10-fold and lowers the input requirement over 100-fold relative to that of ChIA-PET. HiChIP of cohesin reveals multiscale genome architecture with greater signal-to-background ratios than those of in situ Hi-C. ...[more]

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