5C-ID: Increased resolution Chromosome-Conformation-CaptureCarbon-Copy with in situ 3C and double alternating primer design

Mammalian genomes are folded in a hierarchy of compartments, topologically associating domains (TADs), subTADs and looping interactions. Currently, there is a great need to evaluate the link between chromatin topology and genome function across many biological conditions and genetic perturbations. Hi-C generates high quality, high resolution maps of looping interactions genome-wide, but is intractable for high-throughput screening of loops across conditions due to the requirement of an enormous number of reads (>6 Billion) per library. Here, we describe 5C-ID, an updated version of Chromosome-Conformation-Capture-Carbon-Copy (5C) with restriction digest and ligation performed in the nucleus (in situ ChromosomeConformation-Capture (3C)) and ligation-mediated amplification performed with a new double alternating design. 5C-ID reduces spatial noise and enables higher resolution 3D genome folding maps than canonical 5C, allowing for a marked improvement in sensitivity and specificity of loop detection. 5C-ID enables the creation of high-resolution, high-coverage maps of chromatin loops in up to a 30 Megabase subset of the genome at a fraction of the cost of Hi-C.

Dataset features

Information

Specifications

Application:	Hi-C analysis
Number of samples:	7
Release date:	May 7 2018
Last update date:	Nov 20 2018
Access:	Public
Taxon:	Homo sapiens
Dataset link	5C-ID: Increased resolution Chromosome-Conformation-CaptureCarbon-Copy with in situ 3C and double alternating primer design

Experimental Protocol

Total of 7 samples of 5C using double alternating primers, including 1 sample from dilution 3C/5C and 6 samples from different genome copies of in situ 3C/5C

Repositories

GEO

GSE114121

ENA

SRP144756

BioProject

PRJNA464369

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Contact

Jennifer Phillips-Cremins