A scalable, low cost, multi-omic interrogation and sample hashing workflow for single-cell analysis using the Seq-Well S3 platform

ABSTRACT: Clinical samples promise unparalleled insights into the cellular mechanisms that underlie pathological conditions and therapeutic responses. However, they often can be precious, with few cells available for single-cell analysis, necessitating effort to maximize the amount of information that can be garnered from each. Here, we introduce a low material input, cost-effective protocol for conducting multi-omic analyses and sample hashing on single-cell suspensions using the Seq-Well S3 platform. Our protocol, designed to be both accessible and affordable, leverages readily available reagents and standard laboratory equipment, significantly lowering barriers to entry for researchers in low- and middle-income countries. The method detailed herein offers a streamlined and efficient workflow for: (1) precise staining of single-cell suspensions with antibody-oligo conjugates for accurate cell surface protein identification and effective sample multiplexing; (2) reliable generation of Seq-Well S3 sequencing libraries; (3) optional generation of bulk-RNA sequencing libraries through an optimized SMART-seq2 protocol; and, (4) robust computational pipelines for in-depth multi-omic data analysis. This protocol works with fragile and limited cell inputs (here, outlined for 15,000 cells per 200 µL - a fraction of the input required by most commercial methods). It also offers significant cost and time savings, with the entire process from cell isolation to sequencing taking only 3-6 days, plus an additional 1-2 days for data processing. In sum, this generally applicable pipeline empowers researchers around the globe to apply single-cell multiomics to advance their own research agendas.

ORGANISM(S): Homo sapiens

PROVIDER: GSE266385 | GEO | 2024/05/02

REPOSITORIES: GEO