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| Status |
Public on Jun 13, 2017 |
| Title |
Multiplexing droplet-based single cell RNA-sequencing using genetic barcodes |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Here, we introduce an in-silico algorithm demuxlet that harnesses naturally occurring genetic variation in a pool of cells from unrelated individuals to discover the sample identity of each cell and identify droplets containing cells from two different individuals (doublets). These two capabilities enable a simple multiplexing design that increases single cell library construction throughput by experimental design where cells from genetically diverse samples are multiplexed and captured at 2-10x over standard workflows. We further demonstrate the utility of sample multiplexing by characterizing the interindividual variability in cell type-specific responses of ~15k PBMCs to interferon-beta, a potent cytokine. Our computational tool enables sample multiplexing of droplet-based single cell RNA-seq for large-scale studies of population variation and could be extended to other single cell datasets that incorporate natural or synthetic DNA barcodes.
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| Overall design |
HiSeq 2500 data for sequencing of PBMCs from SLE patients and 2 controls. We collected 1M cells each from frozen PBMC samples that were Ficoll isolated and prepared using the 10x Single Cell instrument according to standard protocol. Samples A, B, and C were prepared on the instrument directly following thaw, while samples 2.1 and 2.2 were cultured for 6 hours with (B) or without (A) IFN-beta stimulation prior to loading on the 10x Single Cell instrument.
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| Contributor(s) |
Targ S |
| Citation(s) |
29227470 |
| |
| Submission date |
Mar 14, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Sasha Targ |
| E-mail(s) |
sashatarg@gmail.com
|
| Phone |
6508144110
|
| Organization name |
UCSF IHG
|
| Street address |
513 Parnassus Ave S-965
|
| City |
San Francisco |
| State/province |
California |
| ZIP/Postal code |
94143 |
| 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 |
PRJNA381100 |
| SRA |
SRP102802 |
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