|
| Status |
Public on May 07, 2018 |
| Title |
5C-ID: Increased resolution Chromosome-Conformation-CaptureCarbon-Copy with in situ 3C and double alternating primer design |
| Organism |
Mus musculus |
| Experiment type |
Other
|
| Summary |
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.
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| |
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| Overall design |
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
|
| |
|
| Contributor(s) |
Kim JH, Titus KR, Phillips-Cremins JE |
| Citation(s) |
29772275 |
| |
| Submission date |
May 07, 2018 |
| Last update date |
Mar 25, 2019 |
| Contact name |
Jennifer E Phillips-Cremins |
| E-mail(s) |
jcremins@seas.upenn.edu
|
| Organization name |
University of Pennsylvania
|
| Department |
Bioengineering
|
| Street address |
415 Curie Blvd
|
| City |
Philadelphia |
| State/province |
Pennsylvania |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
|
| Samples (7)
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|
| Relations |
| BioProject |
PRJNA464369 |
| SRA |
SRP144756 |
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