This is probably wishful thinking, but has anyone come across an assay that can measure transcript length without having to run huge gels or by RNA-seq? The former is tedious and not feasible for high-throughput analysis and the latter is super-expensive. I am looking for an assay which will preferably be a 96-well style assay which can measure transcript length accurately. I honestly don't know if this is even possible. I thought of RT-PCR but I wonder if the RT using random primers will bias the PCR measurements towards the full length transcript rather than the truncated one. Any ideas?
Hi Aditi
Although you have elaborated your query quite a bit but still many things are not clear...Are you trying to measure transcript length of a single RNA or a pool of RNAs...is it only mRNAs or any RNA small or big...if you can elaborate these points some approach may be thought about......its feasilibility can be judged later
bye
Have you looked into Agilent Bioanalyzer? It's like running a gel, but on a chip. Each chip only takes 11-12 samples though, so I don't know if this will fit your needs. Sample prep is less tedious and takes less reagents than running gels.
Real time PCR (melt curve) might be used for measuring range of transcript. but for that you should know flanking primers.
If you could re-code the RNA into something that can be run on PacBio then you will have single-molecule measurements up tp ca 4k bp and 200Mb in total per SMRT cell, which costs now (in Europe) ca $300. I am only not sure if such RNA protocol exist - but there are good chances that people experiment with it.
http://www.pacificbiosciences.com/pdf/News_XLChemistryIncreasesReadLengthsThroughput.pdf
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