Assessment of RNA quality

[tabrams]

An important issue concerns assessing RNA quality prior to performing RNAseq on a particular preparation. The Agilent 2100 system does not generate meaningful RIN (RNA Integrity Number) values for Aplysia RNA, or RNA from many invertebrates, apparently because of cleavage of 28S ribosomal RNA. This is a limitation of the software that generates a RIN value, rather than an inherent problem in analyzing samples by electrophoresis.

We would like to evaluate whether low abundance transcripts are intact in specific RNA samples prior to using them for RNAseq. Are there any low abundance messages expressed in CNS that you can suggest could be used a indicators of RNA quality?
(It would be preferable if the transcripts we use as indicators are ones that have already been published or that are available at NCBI.)

[Sathya]

I would consider expression of neuroligin: NM_001204734.1 and CPEB: NM_001204538.1 as candidates. May be we should also include some other genes (that are relatively abundant) whose full length information is available? For example, CEBP, CREB, Kinesin?

[OpheliaCorpEl]

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