Ribo-ITP is a novel strategy that leverages the principles of microfluidics and isotachophoresis (ITP) to fundamentally alter how we isolate ribosome footprints. Specifically, we have designed and manufactured a custom microfluidic polydimethylsiloxane chip to enable simultaneous purification and size selection of RNA fragments using a combination of sieving matrices and ITP, a specialized technique for separation and concentration of small molecules via a nonlinear electrophoretic field. In this study, we have applied Ribo-ITP to characterize translation changes during mouse preimplantation development. The ability to measure ribosome occupancy from single cells and embryos using a sequencing-based ap-proach has uniquely enabled us to characterize allele-specific translation. We used two inbred mouse strains C57BL/6J and CAST/EiJ mice and leveraging strain-specific single nucleo-tide polymorphisms (SNPs), we were able to assign the parent-of-origin for >230k unique ribosome protected footprints.
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