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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: https://doi.org/10.1101/237693
Submission date Dec 19, 2017
Last update date Mar 27, 2019
Contact name Rahul Satija
E-mail(s) rsatija@nygenome.org
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
Relations
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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