No detectable alloreactive transcriptional responses under standard sample preparation conditions during donor-multiplexed single-cell RNA sequencing of peripheral blood mononuclear cells
Abstract
Single-cell RNA sequencing (scRNA-seq) provides high-dimensional measurements of transcript counts in individual cells. However, high assay costs and artifacts associated with analyzing samples across multiple sequencing runs limit the study of large numbers of samples. Sample multiplexing technologies such as MULTI-seq and antibody hashing using single-cell multiplexing kit (SCMK) reagents (BD Biosciences) use sample-specific sequence tags to enable individual samples to be sequenced in a pooled format, markedly lowering per-sample processing and sequencing costs while minimizing technical artifacts. Critically, however, pooling samples could introduce new artifacts, partially negating the benefits of sample multiplexing. In particular, no study to date has evaluated whether pooling peripheral blood mononuclear cells (PBMCs) from unrelated donors under standard scRNA-seq sample preparation conditions (e.g., 30 min co-incubation at 4 °C) results in significant changes in gene expression resulting from alloreactivity (i.e., response to non-self). The ability to demonstrate minimal to no alloreactivity is crucial to avoid confounded data analyses, particularly for cross-sectional studies evaluating changes in immunologic gene signatures.
Document Details
- Document Type
- Pub Defense Publication
- Publication Date
- Jan 20, 2021
- Source ID
- 10.1186/s12915-020-00941-x
Entities
People
- Christopher S. McGinnis
- Chun J. Ye
- David Siegel
- George Hartoularos
- Guorui Xie
- Mars Stone
- Nadia R. Roan
- Sulggi A. Lee
- Zev J Gartner
Organizations
- National Institutes of Health
- National Science Foundation
- United States Department of Defense
- amfAR, The Foundation for AIDS Research