P4-495: SINGLE NUCLEI AND SINGLE WHOLE CELL SEQUENCING OF ALZHEIMER'S DISEASE

With the continued adoption of single cell RNA sequencing, evaluation of parameters and approaches are needed to gauge performance of platforms across sample types and disease conditions. In this study, we evaluated single nuclei RNA sequencing (snRNAseq) and single whole cell RNAseq in quadruplicate on the 10x Chromium platform using fresh frozen frontal cortex from a healthy elderly control and Alzheimer's disease (AD) subject. A median of 1,584 cells or nuclei were sequenced across samples with a median of 31,283 mean reads per cell or nuclei. Corroborating other studies, we observed elevated mitochondrial transcripts, lower levels of intronic sequences, a lower number of genes detected, and increased background, in whole cell libraries compared to nuclei libraries. Upon normalizing the number of reads used for analysis, it was revealed that 5’ priming of mRNA transcripts enabled identification of a larger number of unique genes per cell as well as a larger number of total genes compared to 3’ priming. Utilization of replicates for each sample type improved cell population classification and identified populations include neurons (granule, pyramidal, GABAergic), astrocytes, microglia, endothelial cells, and oligodendrocytes. We further identified two cell populations, oligodendrocyte precursor cells and neuronal stem cells, uniquely in the AD subject. Our evaluation reveals that 5’ snRNAseq demonstrates superior performance on the 10x platform when analyzing fresh frozen brain from elderly subjects. While analysis of larger numbers of samples is needed, we also present preliminary data demonstrating discovery of cell populations in AD.