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Picodroplet partitioned whole genome amplification of low biomass samples preserves genomic diversity for metagenomic analysis

Overview of attention for article published in Microbiome, October 2016
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  • In the top 25% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (88th percentile)
  • Average Attention Score compared to outputs of the same age and source

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1 blog
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17 X users

Citations

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18 Dimensions

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80 Mendeley
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Title
Picodroplet partitioned whole genome amplification of low biomass samples preserves genomic diversity for metagenomic analysis
Published in
Microbiome, October 2016
DOI 10.1186/s40168-016-0197-7
Pubmed ID
Authors

Maria Hammond, Felix Homa, Helene Andersson-Svahn, Thijs J. G. Ettema, Haakan N. Joensson

Abstract

Whole genome amplification (WGA) is a challenging, key step in metagenomic studies of samples containing minute amounts of DNA, such as samples from low biomass environments. It is well known that multiple displacement amplification (MDA), the most commonly used WGA method for microbial samples, skews the genomic representation in the sample. We have combined MDA with droplet microfluidics to perform the reaction in a homogeneous emulsion. Each droplet in this emulsion can be considered an individual reaction chamber, allowing partitioning of the MDA reaction into millions of parallel reactions with only one or very few template molecules per droplet. As a proof-of-concept, we amplified genomic DNA from a synthetic metagenome by MDA either in one bulk reaction or in emulsion and found that after sequencing, the species distribution was better preserved and the coverage depth was more evenly distributed across the genomes when the MDA reaction had been performed in emulsion. Partitioning MDA reactions into millions of reactions by droplet microfluidics is a straightforward way to improve the uniformity of MDA reactions for amplifying complex samples with limited amounts of DNA.

X Demographics

X Demographics

The data shown below were collected from the profiles of 17 X users who shared this research output. Click here to find out more about how the information was compiled.
Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 80 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Brazil 2 3%
Czechia 1 1%
Canada 1 1%
Germany 1 1%
Unknown 75 94%

Demographic breakdown

Readers by professional status Count As %
Researcher 18 23%
Student > Master 13 16%
Student > Ph. D. Student 12 15%
Student > Bachelor 7 9%
Student > Doctoral Student 5 6%
Other 12 15%
Unknown 13 16%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 28 35%
Agricultural and Biological Sciences 21 26%
Immunology and Microbiology 5 6%
Computer Science 2 3%
Engineering 2 3%
Other 7 9%
Unknown 15 19%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 16. 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 22 July 2017.
All research outputs
#2,194,909
of 25,177,382 outputs
Outputs from Microbiome
#867
of 1,727 outputs
Outputs of similar age
#37,082
of 327,102 outputs
Outputs of similar age from Microbiome
#7
of 13 outputs
Altmetric has tracked 25,177,382 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 91st percentile: it's in the top 10% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 1,727 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 38.4. This one is in the 49th percentile – i.e., 49% of its peers scored the same or lower than it.
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 327,102 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 88% of its contemporaries.
We're also able to compare this research output to 13 others from the same source and published within six weeks on either side of this one. This one is in the 46th percentile – i.e., 46% of its contemporaries scored the same or lower than it.