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| 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
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| 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
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| 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.
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| Contributor(s) |
Stoeckius M, Zheng S |
| Citation(s) |
30567574 |
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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
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| Submission date |
Dec 19, 2017 |
| Last update date |
Mar 27, 2019 |
| Contact name |
Soumya Badrinath |
| E-mail(s) |
soumya_badrinath@dfci.harvard.edu
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| Organization name |
Dana-Farber Cancer Institute
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| Street address |
One Jimmy Fund Way
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (5)
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| Relations |
| BioProject |
PRJNA423077 |
| SRA |
SRP127179 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE108313_RAW.tar |
60.4 Mb |
(http)(custom) |
TAR (of CSV, TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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