CooIMPS for robust sequencing of single-nuclear RNAs captured by droplet-based method

Massively-parallel single-cell and single-nucleus RNA sequencing (scRNA-seq, snRNA-seq) requires extensive sequencing to achieve proper per-cell coverage, making sequencing resources and availability of sequencers critical factors for conducting deep transcriptional profiling. CooIMPS is a novel sequencing-by-synthesis approach that relies on nucleotide labeling by re-usable antibodies, but whether it is applicable to snRNA-seq has not been tested. Here, we use a low-cost and off-the-shelf protocol to chemically convert libraries generated with the widely-used Chromium 10X technology to be sequenceable with CooIMPS technology. To assess the quality and performance of converted libraries sequenced with CooIMPS, we generated a snRNA-seq dataset from the hippocampus of young and old mice. Native libraries were sequenced on an Illumina Novaseq and libraries that were converted to be compatible with CooIMPS were sequenced on a DNBSEQ-400RS. CooIMPS-derived data faithfully replicated key characteristics of the native library dataset, including correct estimation of ambient RNA-contamination, detection of captured cells, cell clustering results, spatial marker gene expression, inter- and intra-replicate differences and gene expression changes during aging. In conclusion, our results show that CooIMPS provides a viable alternative to standard sequencing of RNA from dropletbased libraries.

Automated summary

The study introduces a low-cost and off-the-shelf protocol to chemically convert libraries generated with the Chromium 10X technology for sequencing with CooIMPS. By sequencing a snRNA-seq dataset from the hippocampus of mice, it was found that CooIMPS is a viable alternative for accurately replicating key characteristics and detecting gene expression differences.