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10/1/2015

Advantages of RNA-seq over Microarray Technology - Cofactor Genomics

ADVANTAGES OF RNA-SEQ OVER MICROARRAY TECHNOLOGY


By Natalie LaFranzo Posted May 7, 2013In RNA-Seq

Since its inception, RNA-seq has been compared to microarray technology as a means of
generating transcriptome information. Both follow a similar path to answering a biological
question. This begins with experimental design, followed by data acquisition, and finally
analysis and interpretation. However, there are a few key differences between the
technologies, and here at Cofactor, we believe that RNA-seq has a number of advantages.

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10/1/2015

Advantages of RNA-seq over Microarray Technology - Cofactor Genomics

First, using microarray technology limits the researcher to detecting transcripts that
correspond to existing genomic sequencing information. RNA-seq experiments on the other
hand work well for investigating both known transcripts and exploring new ones. Therefore,
RNA-seq is ideal for discovery-based experiments. And while microarrays are limited to the
reference information available during production, RNA-seq experiments may be updated as
new sequence information is obtained.
Second, RNA-seq delivers low background signal. This is because DNA sequences can be
unambiguously mapped to unique regions of the genome. As a result, noise in the experiment
is easily eliminated during analysis. Hybridization issues seen with microarrays, such as crosshybridization or non-ideal hybridization kinetics, are also eliminated in RNA-seq experiments.
This offers another signal-to-noise advantage.
Finally, RNA-seq has the ability to quantify a large dynamic range of expression levels, with
absolute rather than relative values. Even with organisms lacking a reference genome, de

novo transcriptome assembly and differential expression analysis can be performed. There is
no upper limit for this quantification, and at Cofactor, we can help you to determine the
number of reads you need to find the information youre looking for with high levels of
reproducibility between both technical and biological replicates. Whats more, the statistical
analysis we perform can add an additional level of confidence to your results.
Based on current technology, in most cases, the upfront cost of performing a microarraybased experiment will cost less than an RNA-seq based experiment, and may be the most
appropriate solution, based on your goals. However, if the objectives of your experiment
hinge on the three important considerations highlighted above (sensitivity, discovery, range of
expression) RNA-seq is going to be your best bet. This will end up being cheaper and more
time efficient than starting with microarrays and having to end up using RNA-seq later
anyway. By now, most researchers interested in studying gene expression and the dynamic
landscape of the transcriptome have fully adopted RNA-seq for this very reason as well as
many others, not including the aforementioned considerations highlighted in this post.

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10/1/2015

Advantages of RNA-seq over Microarray Technology - Cofactor Genomics

Historically, scientists have shied away from using next-gen sequencing technology due to
worries about successful library preparation and meaningful analysis. To address these
concerns, Cofactors Project Scientists work with you to develop an experimental design that
maximizes the data you obtain at a price youre comfortable with. Our rigorous QC
checkpoints and our extensive experience with library design and preparation (including lowinput/limited material)help us achieve one of the highest success rates in the industry. And
our ActiveSite interface helps you intuitively access and explore the significant amount of data
generated by RNA-seq.
Overall, RNA-seq is a high-throughput, quantitive means of exploring the transcriptome of
your organism of interest. Cofactor is excited and prepared to work with researchers in
academic, government, or industrial labs to leverage our years of experience to design an
experiment that will meet your needs. If youre ready to get started on an RNA-seq project,
were happy to help you reach your research goals.Are you and your team new to RNA-seq?
Schedule a time for us to pay you a visit and provide an introduction to the technology and
our approach.All you have to do is get in touch.
You might also be interested in how Mass Spectrometry stacks up to RNA-seq. Dr. Andy
Benesh covers that in a later blog post.
References:
http://eh.uc.edu/genomics/files/Illumina_Whitepaper_RNASeq_to_arrays_comparison.pdf
http://www.ncbi.nlm.nih.gov/pubmed/?term=19015660
http://www.genomeweb.com/node/1159076

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10/1/2015

Advantages of RNA-seq over Microarray Technology - Cofactor Genomics

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