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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
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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)
  • Good Attention Score compared to outputs of the same age and source (69th percentile)

Mentioned by

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26 tweeters
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5 patents
googleplus
1 Google+ user

Citations

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150 Dimensions

Readers on

mendeley
287 Mendeley
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1 CiteULike
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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 287 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 272 95%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 81 28%
Researcher 64 22%
Student > Bachelor 26 9%
Student > Master 22 8%
Student > Doctoral Student 16 6%
Other 44 15%
Unknown 34 12%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 109 38%
Agricultural and Biological Sciences 94 33%
Computer Science 16 6%
Medicine and Dentistry 10 3%
Physics and Astronomy 4 1%
Other 17 6%
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
#1,180,108
of 22,899,952 outputs
Outputs from Genome Biology (Online Edition)
#1,002
of 4,126 outputs
Outputs of similar age
#17,182
of 267,660 outputs
Outputs of similar age from Genome Biology (Online Edition)
#26
of 82 outputs
Altmetric has tracked 22,899,952 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 4,126 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 75% 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 267,660 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 82 others from the same source and published within six weeks on either side of this one. This one has gotten more attention than average, scoring higher than 69% of its contemporaries.