Sponsored by the AIRR Community

Where do you synthize 5'RACE adaptor with UMI in US?

Protocols
#1

We are trying to include UMI technics in our 5’RACE methods and want to know where do other labs normally buy the oligos from? IDT can do this?
Thanks.

#2

Yes, IDT can synthesize oligos for 5’RACE. Order as “custom RNA oligos”. RNA bases should be written with a lower case “r” in front of them. If your oligo contains deoxyuridine, use “/ideoxyU/”. For example, the oligo that I ordered was:

AAGCAG/ideoxyU/GGTA/ideoxyU/CAACGCAGAG/ideoxyU/NNNN/ideoxyU/NNNN/ideoxyU/NNNN/ideoxyU/CTTrGrGrGrG

(from Turchaninova et al., Nature Protocols 2016)

Also, make sure you select RNase-Free HPLC Purification (available at >=100 nmole scale).

#3

Thanks!

BTW, can I know what the optimized library loading concentration for miseq? We use 14pm and seems it’s too high. Overclustered.