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It sounds like you have considered most of the obvious alternatives (and thank you for clarifying the question). I suppose the first question in an alternatively spliced transcript with a retained intron is whether the open reading frame of the protein is maintained. If there is a termination codon that now becomes in-frame due to the intron then the ...


Qiagen and Life Technologies call it RNA content, total RNA, or total cellular RNA.


Some suggestions. For identifying function do a homology search. There is little functional annotation of lncRNAs. So homology based information can be obtained only for protein sequences. So you can try these: Check the coding potential. Find ORFs (perhaps set a minimum length cutoff). To be stringent you can also check for Kozak consensus sequences (for ...


You can consider use of single-cell RT-qPCR kits such as this one if you have the budget for them. (Note: I have not personally used this kit, just putting out an idea) The Ambion® Single Cell-to-CT™ Kit contains a complete validated workflow for gene expression analysis for samples containing 1–10 cells. Each kit contains reagents for sample ...

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