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Improved DNase-seq protocol facilitates high resolution mapping of DNase I hypersensitive sites in roots in Arabidopsis thaliana

Overview of attention for article published in Plant Methods, September 2015
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Mentioned by

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3 tweeters

Citations

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17 Dimensions

Readers on

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43 Mendeley
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Title
Improved DNase-seq protocol facilitates high resolution mapping of DNase I hypersensitive sites in roots in Arabidopsis thaliana
Published in
Plant Methods, September 2015
DOI 10.1186/s13007-015-0087-1
Pubmed ID
Authors

Jason S. Cumbie, Sergei A. Filichkin, Molly Megraw

Abstract

Identifying cis-regulatory elements is critical in understanding the direct and indirect regulatory mechanisms of gene expression. Current approaches include DNase-seq, a technique that combines sensitivity to the nonspecific endonuclease DNase I with high throughput sequencing to identify regions of regulatory DNA on a genome-wide scale. While this method was originally developed for human cell lines, later adaptations made the processing of plant tissues possible. Challenges still remain in processing recalcitrant tissues that have low DNA content. By removing steps requiring the use of gel agarose plugs in DNase-seq, we were able to significantly reduce the time required to perform the protocol by at least 2 days, while also making possible the processing of difficult plant tissues. We refer to this simplified protocol as DNase I SIM (for simplified in-nucleus method). We were able to successfully create DNase-seq libraries for both leaf and root tissues in Arabidopsis using DNase I SIM. This protocol simplifies and facilitates generation of DNase-seq libraries from plant tissues for high resolution mapping of DNase I hypersensitive sites.

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 43 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 43 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 16 37%
Student > Master 7 16%
Researcher 5 12%
Student > Bachelor 4 9%
Student > Postgraduate 3 7%
Other 6 14%
Unknown 2 5%
Readers by discipline Count As %
Agricultural and Biological Sciences 29 67%
Biochemistry, Genetics and Molecular Biology 11 26%
Computer Science 1 2%
Unknown 2 5%

Attention Score in Context

This research output has an Altmetric Attention Score of 1. 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 05 September 2015.
All research outputs
#2,963,527
of 6,288,002 outputs
Outputs from Plant Methods
#137
of 210 outputs
Outputs of similar age
#105,025
of 193,967 outputs
Outputs of similar age from Plant Methods
#7
of 10 outputs
Altmetric has tracked 6,288,002 research outputs across all sources so far. This one is in the 30th percentile – i.e., 30% of other outputs scored the same or lower than it.
So far Altmetric has tracked 210 research outputs from this source. They typically receive a little more attention than average, with a mean Attention Score of 5.1. This one is in the 20th percentile – i.e., 20% 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 193,967 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 35th percentile – i.e., 35% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 10 others from the same source and published within six weeks on either side of this one. This one has scored higher than 3 of them.