microRNA microarray or small RNASeq

Question

[syrez]

Hi all!

Recently, we were given a choice between microRNA microarray OR small RNASeq for mouse. Upon further discussion, someone raised a question if mouse genome is adequately mapped for microRNA discovery.

Since I'm so new at this, I was wondering if someone else has done small RNA seq to look at microRNAs or if someone can tell me whether small RNA Seq over mouse genome will identify microRNAs?

Thanks! Manish

[syrez]

Ok! Thanks everyone!

Answer 1

[GenoMax]

You have partly answered your own question. On a pre-made array you are limited to interrogating your sample for the content that is already on array. In case of small RNAseq you won't limited by that constraint (but may have additional experimental consideration to think about e.g. libraries). That said, if you are only looking for "known" elements already on the array (and cost, as always) you may decide to go that route.

[User 59]

People are doing small RNA-Seq in organisms that are far worse off in terms of characterisation than the mouse..