RT Journal Article SR Electronic T1 Cell “hashing” with barcoded antibodies enables multiplexing and doublet detection for single cell genomics JF bioRxiv FD Cold Spring Harbor Laboratory SP 237693 DO 10.1101/237693 A1 Marlon Stoeckius A1 Shiwei Zheng A1 Brian Houck-Loomis A1 Stephanie Hao A1 Bertrand Z. Yeung A1 Peter Smibert A1 Rahul Satija YR 2017 UL http://biorxiv.org/content/early/2017/12/21/237693.abstract AB Despite rapid developments in single cell sequencing technology, sample-specific batch effects, detection of cell doublets, and the cost of generating massive datasets remain outstanding challenges. Here, we introduce cell “hashing”, where oligo-tagged antibodies against ubiquitously expressed surface proteins are used to uniquely label cells from distinct samples, which can be subsequently pooled. By sequencing these tags alongside the cellular transcriptome, we can assign each cell to its sample of origin, and robustly identify doublets originating from multiple samples. We demonstrate our approach by pooling eight human PBMC samples on a single run of the 10x Chromium system, substantially reducing our per-cell costs for library generation. Cell “hashing” is inspired by, and complementary to, elegant multiplexing strategies based on genetic variation, which we also leverage to validate our results. We therefore envision that our approach will help to generalize the benefits of single cell multiplexing to diverse samples and experimental designs.