Single-cell analysis of the nervous system at small and large scales with instant partitions

Given the high sequencing costs required to analyze modern, large-scale scRNAseq datasets, particularly with scalable technologies that allow hundreds of thousands of cells to be captured from a single sample, we next examined whether our PIPseq libraries could be sequenced using these alternative sequencing techniques, in line with recent reports26. Aliquots of two PIPseq libraries were sequenced using Ultima technologies’ spinning-wafer high-throughput platform, resulting in 3.1 and 2.2 billion reads per sample (Fig S4D). The Ultima reads were also processed using PIPseeker, and merged Seurat objects with cells sequenced using both platforms were used to probe for any sequencing-platform-based differences (Fig 2G; Fig S4E,F). After integrating using Harmony, we saw no appreciable differences in cell clustering due to the sequencing platform (Fig 2G), thus demonstrating that PIPseq can be successfully used with high-throughput sequencing platforms when analyzing large datasets.