Comprehensive comparative analysis of RNA sequencing methods for degraded or low input samples

DSpace/Manakin Repository

Comprehensive comparative analysis of RNA sequencing methods for degraded or low input samples

Citable link to this page

 

 
Title: Comprehensive comparative analysis of RNA sequencing methods for degraded or low input samples
Author: Adiconis, Xian; Borges-Rivera, Diego; Satija, Rahul; DeLuca, David S.; Busby, Michele A.; Berlin, Aaron M.; Sivachenko, Andrey; Thompson, Dawn Anne; Wysoker, Alec; Fennell, Timothy; Gnirke, Andreas; Pochet, Nathalie; Regev, Aviv; Levin, Joshua Z.

Note: Order does not necessarily reflect citation order of authors.

Citation: Adiconis, X., D. Borges-Rivera, R. Satija, D. S. DeLuca, M. A. Busby, A. M. Berlin, A. Sivachenko, et al. 2013. “Comprehensive comparative analysis of RNA sequencing methods for degraded or low input samples.” Nature methods 10 (7): 10.1038/nmeth.2483. doi:10.1038/nmeth.2483. http://dx.doi.org/10.1038/nmeth.2483.
Full Text & Related Files:
Abstract: RNA-Seq is an effective method to study the transcriptome, but can be difficult to apply to scarce or degraded RNA from fixed clinical samples, rare cell populations, or cadavers. Recent studies have proposed several methods for RNA-Seq of low quality and/or low quantity samples, but their relative merits have not been systematically analyzed. Here, we compare five such methods using metrics relevant to transcriptome annotation, transcript discovery, and gene expression. Using a single human RNA sample, we constructed and sequenced ten libraries with these methods and two control libraries. We find that the RNase H method performed best for low quality RNA, and confirmed this with actual degraded samples. RNase H can even effectively replace oligo (dT) based methods for standard RNA-Seq. SMART and NuGEN had distinct strengths for low quantity RNA. Our analysis allows biologists to select the most suitable methods and provides a benchmark for future method development.
Published Version: doi:10.1038/nmeth.2483
Other Sources: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3821180/pdf/
Terms of Use: This article is made available under the terms and conditions applicable to Other Posted Material, as set forth at http://nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of-use#LAA
Citable link to this page: http://nrs.harvard.edu/urn-3:HUL.InstRepos:11879684
Downloads of this work:

Show full Dublin Core record

This item appears in the following Collection(s)

 
 

Search DASH


Advanced Search
 
 

Submitters