ScholarsArchive@OSU

Citeable URL: http://ir.library.oregonstate.edu/concern/articles/4x51hk87m

This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by BioMed Central. The published article can be found at:  http://www.plantmethods.com/

Additional files can be located online at:  http://www.plantmethods.com/content/11/1/42/additional

Descriptions

Attribute Name	Values
Creator	Megraw, Molly Filichkin, Sergei A. Cumbie, Jason S.
Abstract or Summary	Background: 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. Results: 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. Conclusion: This protocol simplifies and facilitates generation of DNase-seq libraries from plant tissues for high resolution mapping of DNase I hypersensitive sites.
Resource Type	Article
DOI	10.1186/s13007-015-0087-1
Date Available	2015-10-01T13:46:19+00:00
Date Issued	2015-09-04
Citation	Cumbie, J. S., Filichkin, S. A., & Megraw, M. (2015). Improved DNase-seq protocol facilitates high resolution mapping of DNase I hypersensitive sites in roots in Arabidopsis thaliana. Plant Methods, 11(1), 42. doi:10.1186/s13007-015-0087-1
Series	Plant Methods Vol. 11 no. 1
Keyword	Open chromatin Arabidopsis Roots DNase I hypersensitive sites Nuclei DNase-seq
Rights Statement	In Copyright
Funding Statement (additional comments about funding)	This work was supported by the National Institutes of Health [GM097188 to MM]; and by startup funds from Oregon State University.
Publisher	BioMed Central
Peer Reviewed	Yes
Language	English [eng]
Replaces	http://hdl.handle.net/1957/57383
Additional Information	description.provenance : Approved for entry into archive by Patricia Black(patricia.black@oregonstate.edu) on 2015-10-01T13:46:19Z (GMT) No. of bitstreams: 2 license_rdf: 1370 bytes, checksum: cd1af5ab51bcc7a5280cf305303530e9 (MD5) CumbieJasonBotanyPlantPathImprovedDNaseseqProtocol.pdf: 2156244 bytes, checksum: 3ceb457d32029e6a5c85a312c8c67e2d (MD5) description.provenance : Made available in DSpace on 2015-10-01T13:46:19Z (GMT). No. of bitstreams: 2 license_rdf: 1370 bytes, checksum: cd1af5ab51bcc7a5280cf305303530e9 (MD5) CumbieJasonBotanyPlantPathImprovedDNaseseqProtocol.pdf: 2156244 bytes, checksum: 3ceb457d32029e6a5c85a312c8c67e2d (MD5) Previous issue date: 2015-09-04 description.provenance : Submitted by Patricia Black (patricia.black@oregonstate.edu) on 2015-10-01T13:44:27Z No. of bitstreams: 2 license_rdf: 1370 bytes, checksum: cd1af5ab51bcc7a5280cf305303530e9 (MD5) CumbieJasonBotanyPlantPathImprovedDNaseseqProtocol.pdf: 2156244 bytes, checksum: 3ceb457d32029e6a5c85a312c8c67e2d (MD5)

Relationships

Parents:

This work has no parents.

Last modified

Items

Thumbnail	Title	Date Uploaded	Visibility	Actions
	CumbieJasonBotanyPlantPathImprovedDNaseseqProtocol.pdf	2017-07-27	Public	Press to Select an action Download