These indexes get expensive on newer platforms that require unique *dual* indexes (UDIs) for each sample. So how do we sequence more amplicon samples on a single run without racking up 💵 in indexing costs? (3/n)
And CUPID-seq has extra perks! My favorite is that Round 1 PCR products with distinct indexes can be pooled and amplified as part of a single Round 2 PCR reaction. (Caveat: works best when input DNA is at similar concentrations, or Round 1 PCR is driven to saturation.) What's not to love? 💕(8/n)
To solve this problem, we developed CUPID-seq, which uses 🧬🧬two rounds🧬🧬 of unique dual indexing to scale up the number of samples that can be distinguished using a given set of indexes. (4/n)
Dealing with these in-line indexes may seem tricky, but don't worry - we provide a computational pipeline 💻 to demultiplex these indexes and to adapt CUPID-seq to other genomic regions of interest, too. (7/n)