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| Status |
Public on Jan 07, 2020 |
| Title |
Inference and effects of barcode multiplets in droplet-based single-cell assays |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
A widespread assumption for single-cell analyses specifies that one cell’s nucleic acids are predominantly captured by one oligonucleotide barcode. However, we show that ~13-21% of cell barcodes from the 10x Chromium scATAC-seq assay may have been derived from a droplet with more than one oligonucleotide sequence, which we call “barcode multiplets”. We demonstrate that barcode multiplets can be derived from at least two different sources. First, we confirm that approximately 4% of droplets from the 10x platform may contain multiple beads. Additionally, we find that approximately 5% of beads may contain detectable levels of multiple oligonucleotide barcodes. We show that this artifact can confound single-cell analyses, including the interpretation of clonal diversity and proliferation of intra-tumor lymphocytes. Overall, our work provides a conceptual and computational framework to identify and assess the impacts of barcode multiplets in single-cell data.
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| Overall design |
Peripheral blood mononuclear cells were obtained from a healthy individual and processed with 10x scATAC-seq to determine the rate of barcode multiplets
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| Contributor(s) |
Lareau C, Ma S, Duarte F, Buenrostro J |
| Citation(s) |
32054859 |
| |
| Submission date |
Jan 06, 2020 |
| Last update date |
Mar 02, 2020 |
| Contact name |
Caleb Lareau |
| E-mail(s) |
lareauc@mskcc.org
|
| Organization name |
Memorial Sloan Kettering
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| Street address |
417 E 68th St, Zuckerman - ZRC 1132
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| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (1) |
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| Relations |
| BioProject |
PRJNA599177 |
| SRA |
SRP239603 |
