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| Status |
Public on Aug 12, 2015 |
| Title |
Comparison of Hi-C results using in-solution versus in-nucleus ligation |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Other
|
| Summary |
Chromosome conformation capture (3C) and derivative (4C, 5C and Hi-C) methods employ ligation of diluted cross-linked chromatin complexes, intended to favor proximity-dependent, intra-complex ligation. We previously described an alternative Hi-C protocol with ligation in preserved nuclei rather than in solution. Here we directly compare Hi-C methods employing "in-nucleus ligation" and the standard "in-solution ligation". The results show that in-nucleus ligation captures chromatin interactions more consistently over a wider range of distances, and significantly reduces both experimental noise and bias. Thus in-nucleus ligation not only simplifies the experimental procedures, but also produces higher quality data with benefits for the entire range of 3C applications.
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| Overall design |
We created Hi-C libraries by two different methods, in-solution ligation and in-nucleus ligation, from two biological replicates each of mouse foetal liver cells (mouse-1 and mouse-2) and human ES cells (human-1 and human-2) or the mixture of these two species. We also sequenced a random ligation library prepared by reversal of the cross-links and purification of the DNA prior to ligation.
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| Contributor(s) |
Nagano T, Várnai C, Schoenfelder S, Javierre B, Wingett SW, Fraser P |
| Citation(s) |
26306623 |
| |
| Submission date |
Jun 23, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Steven William Wingett |
| E-mail(s) |
steven.wingett@mrc-lmb.cam.ac.uk
|
| Organization name |
MRC Laboratory of Molecular Biology
|
| Department |
Cell Biology
|
| Street address |
Francis Crick Avenue, Cambridge Biomedical Campus
|
| City |
Cambridge |
| State/province |
Cambs |
| ZIP/Postal code |
CB2 0QH |
| Country |
United Kingdom |
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| Platforms (7)
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| GPL11002 |
Illumina Genome Analyzer IIx (Mus musculus) |
| GPL15103 |
Illumina HiSeq 1000 (Mus musculus) |
| GPL15433 |
Illumina HiSeq 1000 (Homo sapiens) |
| GPL15520 |
Illumina MiSeq (Homo sapiens) |
| GPL16417 |
Illumina MiSeq (Mus musculus) |
| GPL19969 |
Illumina MiSeq (Homo sapiens; Mus musculus) |
| GPL20607 |
Illumina HiSeq 1000 (Homo sapiens; Mus musculus) |
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| Samples (13)
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| GSM1718020 |
Human sample1: Hi-C in-nucleus ligation |
| GSM1718021 |
Human sample1: Hi-C in-solution ligation |
| GSM1718022 |
Human sample2: Hi-C in-nucleus ligation |
| GSM1718023 |
Human sample2: Hi-C in-solution ligation |
| GSM1718024 |
Mouse sample1: Hi-C in-nucleus ligation |
| GSM1718025 |
Mouse sample1: Hi-C in-solution ligation |
| GSM1718026 |
Mouse sample2: Hi-C in-nucleus ligation |
| GSM1718027 |
Mouse sample2: Hi-C in-solution ligation |
| GSM1718028 |
Mouse random Hi-C ligation |
| GSM1718029 |
Mouse-human mixture1: Hi-C in-nucleus ligation |
| GSM1718030 |
Mouse-human mixture1: Hi-C in-solution ligation |
| GSM1718031 |
Mouse-human mixture2: Hi-C in-nucleus ligation |
| GSM1718032 |
Mouse-human mixture2: Hi-C in-solution ligation |
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| Relations |
| BioProject |
PRJNA287806 |
| SRA |
SRP059793 |
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