↓ Skip to main content

Comparison of Hi-C results using in-solution versus in-nucleus ligation

Overview of attention for article published in Genome Biology (Online Edition), August 2015
Altmetric Badge

About this Attention Score

  • In the top 25% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (93rd percentile)

Mentioned by

twitter
26 tweeters
patent
5 patents
googleplus
1 Google+ user

Citations

dimensions_citation
149 Dimensions

Readers on

mendeley
280 Mendeley
citeulike
1 CiteULike
You are seeing a free-to-access but limited selection of the activity Altmetric has collected about this research output. Click here to find out more.
Title
Comparison of Hi-C results using in-solution versus in-nucleus ligation
Published in
Genome Biology (Online Edition), August 2015
DOI 10.1186/s13059-015-0753-7
Pubmed ID
Authors

Takashi Nagano, Csilla Várnai, Stefan Schoenfelder, Biola-Maria Javierre, Steven W. Wingett, Peter Fraser

Abstract

Chromosome conformation capture and various derivative methods such as 4C, 5C and Hi-C have emerged as standard tools to analyze the three-dimensional organization of the genome in the nucleus. These methods employ ligation of diluted cross-linked chromatin complexes, intended to favour proximity-dependent, intra-complex ligation. During development of single-cell Hi-C, we devised 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 with the standard in-solution ligation. We show in-nucleus ligation results in consistently lower levels of inter-chromosomal contacts. Through chromatin mixing experiments we show that a significantly large fraction of inter-chromosomal contacts are the result of spurious ligation events formed during in-solution ligation. In-nucleus ligation significantly reduces this source of experimental noise, and results in improved reproducibility between replicates. We also find that in-nucleus ligation eliminates restriction fragment length bias found with in-solution ligation. These improvements result in greater reproducibility of long-range intra-chromosomal and inter-chromosomal contacts, as well as enhanced detection of structural features such as topologically associated domain boundaries. We conclude that in-nucleus ligation captures chromatin interactions more consistently over a wider range of distances, and significantly reduces both experimental noise and bias. In-nucleus ligation creates higher quality Hi-C libraries while simplifying the experimental procedure. We suggest that the entire range of 3C applications are likely to show similar benefits from in-nucleus ligation.

Twitter Demographics

The data shown below were collected from the profiles of 26 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 280 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United Kingdom 4 1%
United States 2 <1%
Norway 2 <1%
France 1 <1%
Lithuania 1 <1%
Portugal 1 <1%
Canada 1 <1%
Germany 1 <1%
Japan 1 <1%
Other 1 <1%
Unknown 265 95%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 80 29%
Researcher 62 22%
Student > Bachelor 26 9%
Student > Master 22 8%
Student > Doctoral Student 14 5%
Other 42 15%
Unknown 34 12%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 106 38%
Agricultural and Biological Sciences 94 34%
Computer Science 15 5%
Medicine and Dentistry 10 4%
Physics and Astronomy 4 1%
Other 14 5%
Unknown 37 13%

Attention Score in Context

This research output has an Altmetric Attention Score of 28. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 23 June 2021.
All research outputs
#1,082,350
of 21,399,109 outputs
Outputs from Genome Biology (Online Edition)
#946
of 3,965 outputs
Outputs of similar age
#16,240
of 253,317 outputs
Outputs of similar age from Genome Biology (Online Edition)
#1
of 1 outputs
Altmetric has tracked 21,399,109 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 94th percentile: it's in the top 10% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 3,965 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 27.6. This one has done well, scoring higher than 76% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 253,317 tracked outputs that were published within six weeks on either side of this one in any source. This one has done particularly well, scoring higher than 93% of its contemporaries.
We're also able to compare this research output to 1 others from the same source and published within six weeks on either side of this one. This one has scored higher than all of them