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A simple method for semi-random DNA amplicon fragmentation using the methylation-dependent restriction enzyme MspJI

Overview of attention for article published in BMC Biotechnology, April 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 (86th percentile)

Mentioned by

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1 news outlet
twitter
3 tweeters

Citations

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13 Dimensions

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30 Mendeley
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Title
A simple method for semi-random DNA amplicon fragmentation using the methylation-dependent restriction enzyme MspJI
Published in
BMC Biotechnology, April 2015
DOI 10.1186/s12896-015-0139-7
Pubmed ID
Authors

Hiroshi Shinozuka, Noel O I Cogan, Maiko Shinozuka, Alexis Marshall, Pippa Kay, Yi-Han Lin, German C Spangenberg, John W Forster

Abstract

Fragmentation at random nucleotide locations is an essential process for preparation of DNA libraries to be used on massively parallel short-read DNA sequencing platforms. Although instruments for physical shearing, such as the Covaris S2 focused-ultrasonicator system, and products for enzymatic shearing, such as the Nextera technology and NEBNext dsDNA Fragmentase kit, are commercially available, a simple and inexpensive method is desirable for high-throughput sequencing library preparation. MspJI is a recently characterised restriction enzyme which recognises the sequence motif CNNR (where R = G or A) when the first base is modified to 5-methylcytosine or 5-hydroxymethylcytosine. A semi-random enzymatic DNA amplicon fragmentation method was developed based on the unique cleavage properties of MspJI. In this method, random incorporation of 5-methyl-2'-deoxycytidine-5'-triphosphate is achieved through DNA amplification with DNA polymerase, followed by DNA digestion with MspJI. Due to the recognition sequence of the enzyme, DNA amplicons are fragmented in a relatively sequence-independent manner. The size range of the resulting fragments was capable of control through optimisation of 5-methyl-2'-deoxycytidine-5'-triphosphate concentration in the reaction mixture. A library suitable for sequencing using the Illumina MiSeq platform was prepared and processed using the proposed method. Alignment of generated short reads to a reference sequence demonstrated a relatively high level of random fragmentation. The proposed method may be performed with standard laboratory equipment. Although the uniformity of coverage was slightly inferior to the Covaris physical shearing procedure, due to efficiencies of cost and labour, the method may be more suitable than existing approaches for implementation in large-scale sequencing activities, such as bacterial artificial chromosome (BAC)-based genome sequence assembly, pan-genomic studies and locus-targeted genotyping-by-sequencing.

Twitter Demographics

The data shown below were collected from the profiles of 3 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 30 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United Kingdom 1 3%
Italy 1 3%
Unknown 28 93%

Demographic breakdown

Readers by professional status Count As %
Researcher 10 33%
Student > Ph. D. Student 5 17%
Student > Bachelor 5 17%
Student > Master 4 13%
Student > Doctoral Student 2 7%
Other 2 7%
Unknown 2 7%
Readers by discipline Count As %
Agricultural and Biological Sciences 18 60%
Biochemistry, Genetics and Molecular Biology 9 30%
Immunology and Microbiology 1 3%
Unknown 2 7%

Attention Score in Context

This research output has an Altmetric Attention Score of 12. 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 19 April 2015.
All research outputs
#2,208,227
of 19,211,930 outputs
Outputs from BMC Biotechnology
#76
of 884 outputs
Outputs of similar age
#32,929
of 238,042 outputs
Outputs of similar age from BMC Biotechnology
#1
of 1 outputs
Altmetric has tracked 19,211,930 research outputs across all sources so far. Compared to these this one has done well and is in the 88th percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 884 research outputs from this source. They typically receive a little more attention than average, with a mean Attention Score of 6.6. This one has done particularly well, scoring higher than 91% 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 238,042 tracked outputs that were published within six weeks on either side of this one in any source. This one has done well, scoring higher than 86% 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