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Series GSE108313 Query DataSets for GSE108313
Status Public on Jan 02, 2018
Title Cell hashing enable sample multiplexing, multiplet identification and super-loading on droplet-based single cell RNA-sequencing platforms
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary We reasoned that by using a distinct set of oligo-tagged antibodies against ubiquitously expressed proteins, we could uniquely label multiple populations of cells, multiplex them together, and use the barcoded antibody signal as a fingerprint. We refer to this approach as cellular "hashing", as our set of oligos defines a "look up table" to assign each multiplexed cell to its original sample. We demonstrate application of the technique to combine eight samples and run them simultaneously in a single droplet based scRNA-seq run. We show that cell hashtags allow sample multiplexing, confident multiplet identification and super-loading in the context of a commonly used droplet-based scRNA-seq method to drive down the per-cell cost of large-scale scRNA-seq experiments
Overall design We chose a set of monoclonal antibodies directed against ubiquitously and highly expressed immune surface markers (CD45, CD98, CD44, and CD11a) and combined these antibodies into eight identical pools (pool A-H), and subsequently conjugated each pool to a distinct hashtag oligonucleotide (henceforth referred to as HTOs). The HTOs contain a unique 10- or 12-bp barcode that could be read out and linked to the cellular transcriptome, through minor modifications to standard scRNA-seq protocols.
Contributor(s) Stoeckius M, Zheng S
Citation(s) 30567574
M Stoeckius, S Zheng, B Houck-Loomis, S Hao, B Yeung, P Smibert, and R Satija. Cell hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics. bioRxiv 237693; doi:
Submission date Dec 19, 2017
Last update date Mar 27, 2019
Contact name Rahul Satija
Organization name New York Genome Center
Street address 101 Avenue of the Americas
City New York
State/province NY
ZIP/Postal code 10013
Country USA
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (5)
GSM2895282 Hashtag-RNA
GSM2895283 Hashtag-HTO
GSM2895284 Hashtag-ADT
BioProject PRJNA423077
SRA SRP127179

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Supplementary file Size Download File type/resource
GSE108313_RAW.tar 60.4 Mb (http)(custom) TAR (of CSV, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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