Difference Between RNA Seq and Microarray

The main difference between RNA Seq and microarray is that the RNA Seq (RNA Sequencing) allows analyzing novel RNA and RNA variants whereas the microarray allows analyzing the transcriptome with the use of known RNA probes. Furthermore, RNA Seq is a sequencing-based technique while microarray is based on hybridization.

RNA Seq and microarray are two techniques used to analyze the transcriptome, which is the total mRNA expressed of an organism. They allow determining the types of RNA molecules formed at a defined cellular stage.

Key Areas Covered

1. What is RNA Seq
     – Definition, Process, Significance
2. What is Microarray
     – Definition, Process, Significance
3. What are the Similarities Between RNA Seq and Microarray
     – Outline of Common Features
4. What is the Difference Between RNA Seq and Microarray
     – Comparison of Key Differences

Key Terms

Gene Expression Analysis, Hybridization, Microarray, RNA Seq, Sequencing

What is RNA Seq

RNA Seq (RNA sequencing) is a technique that determines the sequence of RNA molecules in a sample. RNA Seq involves high-throughput shotgun sequencing of cDNA molecules. cDNA is obtained from the reverse transcription of the RNA molecules. Next-generation sequencing involves the determination of the sequence of cDNA. RNA Seq allows the determination of the RNA sequence and their relative abundance.

Figure 1: RNA Seq Process

RNA Seq is a highly reliable technique with a wide range of sensitivity. Hence, it can detect rare and low abundant RNA sequences. The unique feature of RNA Seq is its ability to identify novel RNA sequences and the splicing variants.

What is Microarray

Microarray is a technique widely used to analyze the gene expression of a particular organism. It uses defined probes that are hybridized with the RNA molecules in the sample. The single stranded probes are attached to a solid surface known as a chip to which the fluorescent labelled RNA sample is hybridized with. Genome sequencing data can be used to design probes.

Figure 2: Microarray Process

For a quick and easy experiment, microarray is the best technique in the gene expression analysis. But, the probes have to be designed in such a way to detect splicing variants as well.

Similarities Between RNA Seq and Microarray

• RNA Seq and microarray are two techniques used in the gene expression analysis.
• They can detect the types of RNA molecules present in a sample at a defined time.
• They depend on the RNA sequence.
• Both techniques can determine the primary sequence and the relative abundance of the RNA in a sample.
• Reproducibility of both techniques is high.

Difference Between RNA Seq and Microarray

Definition

The RNA Seq refers to a sequencing-based technique that detects the RNA sequences in a sample while the microarray refers to a hybridization-based technique used to detect the presence of specific RNA sequences within a sample.

Based on

RNA Seq is a sequencing-based technique while microarray is a hybridization-based technique done with existing probes.

Identifying New Sequences

The RNA Seq can identify new RNA sequences present in a sample while microarray can only identify known sequences.

Sensitivity

Sensitivity of RNA Seq is high while the sensitivity of microarray is comparatively low.

Accuracy

The accuracy of the RNA Seq data is high while the accuracy of the microarray data is comparatively low.

SNP Detection

RNA Seq can identify SNP except de novo SNPs for low abundance RNAs while microarray cannot detect SNPs.

Cost

The RNA Seq is expensive ($300-$1000/sample) due to the extensive bioinformatic analysis required by the method while microarray is less expensive ($100-200/sample).

Conclusion

RNA Seq is a sequencing-based technique used to determine the RNA sequences present in the transcriptome while microarray uses specific probes to detect the presence of particular sequences in the transcriptome. Microarray cannot detect any novel RNA sequences as well as less abundant RNA sequences. But, in RNA Seq, all the RNA sequences within the sample can be identified. Therefore, the main difference between RNA Seq and microarray is the type of detection.

Reference:

1. Kukurba, Kimberly R., and Stephen B. Montgomery. “RNA Sequencing and Analysis.” Cold Spring Harbor protocols 2015.11 (2015): 951–969. PMC. Web. 3 July 2018, Available Here
2. Govindarajan, Rajeshwar et al. “Microarray and Its Applications.” Journal of Pharmacy & Bioallied Sciences 4.Suppl 2 (2012): S310–S312. PMC. Web. 3 July 2018, Available Here

Image Courtesy:

1. “Summary of RNA-Seq” By Thomas Shafee – Own work (CC BY 4.0) via Commons Wikimedia
2. “Summary of RNA Microarray” By Thomas Shafee – Own work (CC BY 4.0) via Commons Wikimedia