Designing not-so-random MULTI-seq barcodes
I’m trying to perform single-nucleus RNA-seq on nuclei isolated from early postnatal mouse cortex. I plan to use MULTI-seq barcodes to label nuclei from a given individual, then pool individuals for one 10X 3′ single nucleus RNA-seq run.
The MULTI-seq paper (McGinnis et al. 2019; www.nature.com/articles/s41592-019-0433-8) provides the sequence of the barcode oligos (including a polyA region, PCR handle, and the barcode itself). The 8bp sequence corresponding to the barcode consists of 8 Ns, denoting random nucleotides, but I don’t necessarily want the barcodes to be entirely random for a couple reasons. Most importantly, I want to minimize dimerization and off-target hybridization.
Anyone know of a list of tested multi-seq barcodes for use in mice? Or I’m thinking there’s got to be some way for me to test barcodes in silico? Any help appreciated, TIA
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