Assistant prof at UC Irvine. Ecology and evolution in microbial communities, and occasional writing.
https://kxuelab.com
Katherine Xue
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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)
Katherine Xue
New sequencing platforms have higher throughput and lower sequencing costs - but amplicon libraries don't always benefit. In practice, the number of amplicon libraries on a sequencing run is usually limited by the number of unique DNA indexes. (2/n)
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)
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)
CUPID-seq is built on a familiar, two-step PCR strategy for building amplicon libraries - but with the twist that there are multiple sets of Round 1 primers, each pair carrying a distinct UDI. (5/n)
Infinite love to the amazing Beverly Fu and Rachel Porter, who wrote the experimental and computational protocols; Handuo Shi, Allison Ea, Ana Espeleta, Achuthan Ambat, who tested and expanded CUPID-seq; and David Relman and KC Huang, who helped me develop and test this idea. 💗🧬 (n/n)
The Xue lab at UC Irvine is looking for a staff scientist to support our work investigating how microbes interact and evolve in the gut microbiome! Open to a wide range of previous experience levels, see ad for more.
recruit.ap.uci.edu/JPF09601
Do you love amplicon sequencing? Do you want to sequence MORE amplicons, faster and at lower cost? Check out 💘CUPID-seq💘, a highly multiplexed library design that lets you sequence hundreds of amplicon samples (16S, 18S, and more!) on a single sequencing run! (1/n) 🧵 www.biorxiv.org/content/10.6...
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)
