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. 2012 Dec 28;3(1):9.
doi: 10.1186/1758-907X-3-9.

Strand-specific libraries for high throughput RNA sequencing (RNA-Seq) prepared without poly(A) selection

Zhao Zhang  1 , William E Theurkauf, Zhiping Weng, Phillip D Zamore
Affiliations

Strand-specific libraries for high throughput RNA sequencing (RNA-Seq) prepared without poly(A) selection

Zhao Zhang et al. Silence. .

Abstract

Background: High throughput DNA sequencing technology has enabled quantification of all the RNAs in a cell or tissue, a method widely known as RNA sequencing (RNA-Seq). However, non-coding RNAs such as rRNA are highly abundant and can consume >70% of sequencing reads. A common approach is to extract only polyadenylated mRNA; however, such approaches are blind to RNAs with short or no poly(A) tails, leading to an incomplete view of the transcriptome. Another challenge of preparing RNA-Seq libraries is to preserve the strand information of the RNAs.

Design: Here, we describe a procedure for preparing RNA-Seq libraries from 1 to 4 μg total RNA without poly(A) selection. Our method combines the deoxyuridine triphosphate (dUTP)/uracil-DNA glycosylase (UDG) strategy to achieve strand specificity with AMPure XP magnetic beads to perform size selection. Together, these steps eliminate gel purification, allowing a library to be made in less than two days. We barcode each library during the final PCR amplification step, allowing several samples to be sequenced in a single lane without sacrificing read length. Libraries prepared using this protocol are compatible with Illumina GAII, GAIIx and HiSeq 2000 platforms.

Discussion: The RNA-Seq protocol described here yields strand-specific transcriptome libraries without poly(A) selection, which provide approximately 90% mappable sequences. Typically, more than 85% of mapped reads correspond to protein-coding genes and only 6% derive from non-coding RNAs. The protocol has been used to measure RNA transcript identity and abundance in tissues from flies, mice, rats, chickens, and frogs, demonstrating its general applicability.

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Figures

Figure 1
Figure 1
Protocol workflow.
Figure 2
Figure 2
Library and sequencing primer sequences.
Figure 3
Figure 3
Anticipated results. (A) Bioanalyzer plot. (B) Agarose gel for small-scale colony sequencing. Control, a PCR reaction with no bacterial colony added.
See this image and copyright information in PMC

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