10/1/2015 Advantages of RNA-seq over Microarray Technology - Cofactor Genomics

https://cofactorgenomics.com/advantages-rna-seq-over-microarray-technology/ 1/4

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

ADVANTAGES OF RNA-SEQ OVER MICROARRAY TECHNOLOGY

Since it’s 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.

10/1/2015 Advantages of RNA-seq over Microarray Technology - Cofactor Genomics

https://cofactorgenomics.com/advantages-rna-seq-over-microarray-technology/ 2/4

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 cross-

hybridization 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 you’re looking for with high levels of

reproducibility between both technical and biological replicates. What’s 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 microarray-

based 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.

10/1/2015 Advantages of RNA-seq over Microarray Technology - Cofactor Genomics

https://cofactorgenomics.com/advantages-rna-seq-over-microarray-technology/ 3/4

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, Cofactor’s Project Scientists work with you to develop an experimental design that

maximizes the data you obtain at a price you’re comfortable with. Our rigorous QC

checkpoints and our extensive experience with library design and preparation (including low-

input/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 you’re ready to get started on an RNA-seq project,

we’re 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

Related

10/1/2015 Advantages of RNA-seq over Microarray Technology - Cofactor Genomics

https://cofactorgenomics.com/advantages-rna-seq-over-microarray-technology/ 4/4

Powered by

6 Changes That'll Make a BigDifference With Your RNA­

seq; Part 5

How noisy is your RNA­seqprocess? ­ An in­depth look at

process noise.

6 Changes That'll Make a BigDifference With Your RNA­

seq; Part 6

Explore Cofactor Genomics

Cofactor to introduce world'sfirst bovine exome capture

product

6 Changes That'll Make a BigDifference With Your RNA­

seq; Part 1

6 Changes That'll Make a BigDifference With Your RNA­

seq; Part 3