Specifically for miRNA, but also interested in RNA in general
Hi Marc
To cut a long story short, I will tell you that with no doubts NGS will give you better results for miRNAs, but still you have to pay the price. Microarrays suffer from the typical noise which is related with the inherent characteristics of miRNAs (very short sequences). In microarrays you will get a good signal from miRNAs that are abundant in your samples, but you will probably miss less abundant species. If you want to do microarrays I will suggest you to use LNA probes (Exiqon) to improve sensitivity.
About using NGS for miRNAs, you will get everything, including the low abundance species. Following Murphy's law, they are normally the most important when you are dealing with a particular biological processes. Be careful if you want to apply NGS for characterization of circulating miRNAs, since these protocols are still not very well defined and the amount of RNA in the samples is normally very low.
About mRNAs and ncRNAs transcripts, the microarrays are still a good and solid technology and you must have no fear to use it. The main advantage is that microarray data processing is very easy, the software is very robust, and easy to use. The disadvantage is that you are biased because of the use of probes that just will catch the transcripts present in the array.
On the contrary, in NGS for transcriptomic studies, you would probably need the help of a bioinformatician. The software for data processing is not so user friendly and rapidly evolving, but you will get everything that is within the sample.
So.. everything depends on money and technical issues. Hope that it helps.
Be free to contact me if you need further info or help. Take care. Best
Paco
Hi Marc
To cut a long story short, I will tell you that with no doubts NGS will give you better results for miRNAs, but still you have to pay the price. Microarrays suffer from the typical noise which is related with the inherent characteristics of miRNAs (very short sequences). In microarrays you will get a good signal from miRNAs that are abundant in your samples, but you will probably miss less abundant species. If you want to do microarrays I will suggest you to use LNA probes (Exiqon) to improve sensitivity.
About using NGS for miRNAs, you will get everything, including the low abundance species. Following Murphy's law, they are normally the most important when you are dealing with a particular biological processes. Be careful if you want to apply NGS for characterization of circulating miRNAs, since these protocols are still not very well defined and the amount of RNA in the samples is normally very low.
About mRNAs and ncRNAs transcripts, the microarrays are still a good and solid technology and you must have no fear to use it. The main advantage is that microarray data processing is very easy, the software is very robust, and easy to use. The disadvantage is that you are biased because of the use of probes that just will catch the transcripts present in the array.
On the contrary, in NGS for transcriptomic studies, you would probably need the help of a bioinformatician. The software for data processing is not so user friendly and rapidly evolving, but you will get everything that is within the sample.
So.. everything depends on money and technical issues. Hope that it helps.
Be free to contact me if you need further info or help. Take care. Best
Paco
I fully agree with Francisco. NGS allows you to see fusions or other structural rearrangements should they be present e.g. in cancer. If you are just looking for differential expression, arrays are fine albeit becoming dated.
Agree with above. NGS will give you more options but require expertise maybe also custom scripts for analysis. For sequencing library you can use e.g. NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) followed by e.g. Illumina MiSeq.
What's your experiment and biological question? Which species?
Technologies are just tools with different strengths and weaknesses. It is true that NGS is almost a complete superset of microarrays. However, depending on the experiment, question and species microarray might be suitable.
Francisco Enguita has alluded to the NGS and arrays for miRNA discovery; however as Christian Cole says, it is context dependent. You have to define your basic biological question, resources, including technical expertise and money and the time allotted to reach an answer before you go for the arrays or the NGS. For routine mIRNA comparisons arrays are well tested and Exiqon (now Dharmacon) LNA technology gives good specificity and noise control. However if the aim is to screen for novel miRNAs that are hitherto not known and may not express in high levels the NGS is the better choice. Choose your bait !!!
Thank you Francisco, William, Hans, Christian, and Shahid for your answers and general comments and opinions, I think we will proceed with NGS.
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