Small RNA 5' adapters with barcodes?

[bscruggs]

I'm prepping a small RNA library with the TruSeq Small RNA library kit. I typically use the RA5 adapter provided in the kit. For my current experiment, I need a second 5' adapter that I can distinguish from RA5.

I want to ligate one 5' adapter onto one RNA class and a second distinct 5' adapter onto a different RNA class. Each adapter needs to have a region of unique sequence so they can be distinguished. Any recommendations for barcoded adapters like this? Or thoughts on how they should be designed? Thanks!

[kerplunk412]

Can you please explain why you need to do this during the adapter ligation step? It seems you could just prep two different libraries with different barcodes.

As the 5' adapter contains the sequencing primer binding site, the only way I think you could barcode 5' adapters is with an in-line barcode at the ligation site. However, there is a large body of literature that shows adapter sequences are a major source of bias in small RNA library preps, especially the bases near the ligation junction, so I would strongly discourage using different 5' adapters if you are trying to directly compare the results.