Hi, Ravi

well it depends on your way of RNA extraction. if you extract total RNA just follow the basic RNA checking tests namely 260/280 spectrophotometry and running on agaros gel . if you want to go further, checking highly expressing microRNA is a good option. expression level of miRs that usually are used as internal control like miR-15, miR-103 and miR-191 could positively reflect tested sample quality.

You may want to analyze the intigrety of your total RNAs in order to verify whether your samples are good to perform downstream experiments. It can be done by using a bioanalyzer platform (https://www.genomics.agilent.com/en/Bioanalyzer-System/2100-Bioanalyzer-Instruments/?cid=AG-PT-106). You must not have problems if you want to analyze miRNAs directly without qualification of your RNAs because they are resistant to degradation. Nevertheless for lncRNA you need good integrity of your RNAs.

Thank you, all for your suggestions. We typically use the Agilent RNA isolation kit, although the group with which we are working uses the Qiagen RNA isolation kit. We are now QCing based on RNA isolated from the Qiagen kit.  We did use the bioanalyzer and the integrity looked good for 3 of the 4 cell populations. The fourth population had some RNA degradation and very low yield. We are actively working to improve yield/quality of RNA isolated from the fourth population.

I would like to asses the quality of miRNA and lncRNA in the RNA from the 3 populations that looked good (and gave good RNASeq reads). I will ask our core folks about getting in the small RNA chip for the bioanalyzer.

We are really pushing the limits of the technology using primary cell populations which are quite small and therefore do not have a lot of RNA per cell. So we need to prove to ourselves that we can get enough quality RNA from that fourth sample and assess the quality of miRNA nd lncRNA from the three other populations.