4 replies to this topic

[AminoAcylTRNASynthetase]

Hi everybody,

Does anyone know a database, where I can search for verified RNAi Sequences for siRNA, shRNA and miRNA?

Thanks for any help.

Greetings
AAtRS

[pcrman]

You can search validated shRNA from Sigma Mission shRNA https://www.sigmaald...-and-order.html. If you want to use siRNA instead of shRNA, you can infer siRNA targets out of the shRNA sequence.

[warsel]

Hmm.. to my knowledge these are from the RNAi Consortium Sets/Dave Root - I was under the impression that this TRCN set is not completely validated.
Are you sure there is validation data for all constructs - if yes, where do I find it on the Sigma website?

[Functional Screens]

Sigma's web site marked some shRNA sequences as "validated", but I wonder how they validated (reporter assay, qRT-PCR, or Western blot) and which one is the potent one.  They are from TRC and the algorithm is old.

[warsel]

The TRCN are validated by qPCR as far as I know (we got some of that data from TRCN directly) - overall knockdown efficiency in that dataset is between 20 and 90% from what I have seen - so quite variable if you want to use only one or two vectors.

I wondered if Sigma would have done some additional QC on that - seems they didn't.

Edited by warsel, 25 November 2009 - 04:16 AM.