Abstract 334: Flexible and high-throughput microwell-based single-cell capture for multiomic ATAC-seq and RNA-seq profiling
Authors: Rosary Nguyen, Hongduan Huang, Quyen Bao, Punya Narayan, Hye-Won Song, Elham Hatami, Zhiqi Zhang, Thomas McCarthy, Youngsook Kim, Ruifang Li, Chelsea Gordon, Larry Wang, Aruna Ayer
Journal: Cancer Research (2024)

Abstract The simultaneous profiling of chromatin accessibility and gene expression is an active area of interest for researchers studying how epigenetic changes regulate gene expression at the single-cell level. Here, we demonstrate the feasibility of single nuclei assay for transposase-accessible chromatin (snATAC) seq either with or without simultaneous gene expression profiling using the microwell-based BD Rhapsody™ HT Xpress System. Taking advantage of an eight-lane microwell cartridge, the BD Rhapsody™ HT Xpress System can support the snATAC seq assay with nuclei input ranging from 1,000 to 400,000 nuclei in a single experiment. To demonstrate the flexible throughput capabilities, 1,000 to 50,000 nuclei from cryopreserved peripheral blood mononuclear cells (PBMCs) were tagmented and loaded onto a single lane of the BD Rhapsody™ HT Xpress System. The snATAC assay libraries were prepared and sequenced, revealing multiple high-quality ATAC-seq metrics: high counts of unique ATAC fragments, high fraction of reads in peak regions (FRiP), and high transcriptional start site (TSS) enrichment score. The data were obtained consistently across the wide range of input nuclei with use of the gentle and robust nuclei loading capabilities of the BD Rhapsody™ HT Xpress System. Moreover, after capturing ATAC fragments, the BD Rhapsody™ Enhanced Cell Capture Beads are stable and can be stored at 4 °C for up to 3 months, allowing researchers the flexibility in sequencing subsets of nuclei or lanes for QC purposes before sequencing the entire library and returning to samples for complete sequencing. Furthermore, to demonstrate the consistency of both open chromatin profiling and mRNA gene expression as a combination (multiomic snATAC + snRNAseq), firstly, we compared snRNAseq data from a whole transcriptome assay (WTA) with snRNAseq from an ATAC+mRNA multiomic assay using the same sample. This strategy enabled us to show that there is negligible gene expression differences between snRNAseq from the BD whole transcriptome assay and snRNAseq from the multiomic scATAC and scRNA assay. Likewise, the snATACseq assay and snATACseq assay with simultaneous whole transcriptome profiling shows that chromatin accessibility profiling is equivalent with and without gene expression profiling. Enabling this new scATAC assay on the BD Rhapsody™ HT Xpress System can advance the study of epigenetic regulation of gene expression with a robust and flexible workflow. This will allow researchers to analyze both open chromatin and mRNA at varying nuclei inputs with single-cell resolution to understand the underlying molecular mechanisms in gene expression regulatory pathways. This assay can be readily extended to broader samples to gain greater understanding of disease states in immunology and immuno-oncology studies. For Research Use Only. Not for use in diagnostic or therapeutic procedures. © 2023 BD. All rights reserved. Citation Format: Rosary Nguyen, Hongduan Huang, Quyen Bao, Punya Narayan, Hye-Won Song, Elham Hatami, Zhiqi Zhang, Thomas McCarthy, Youngsook Kim, Ruifang Li, Chelsea Gordon, Larry Wang, Aruna Ayer. Flexible and high-throughput microwell-based single-cell capture for multiomic ATAC-seq and RNA-seq profiling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 334.