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| Status |
Public on Jan 15, 2021 |
| Title |
Systematic comparison of high-throughput single-cell RNA-seq methods for immune cell profiling [icell8] |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
We systematically benchmarked seven high-throughput single-cell RNA-seq methods. We prepared 21 libraries under identical conditions of a defined mixture of two human and two murine lymphocyte cell lines, simulating heterogeneity across immune-cell types and cell sizes. We evaluate methods by their cell recovery rate, library efficiency, sensitivity, and ability to recover expression signatures for each cell type. We observed higher mRNA detection sensitivity with the 10x Genomics 5’ v1 and 3’ v3 methods. We demonstrate that these methods have fewer drop-out events which facilitates the identification of differentially-expressed genes and improves the concordance of single-cell profiles to immune bulk RNA-seq signatures.
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| Overall design |
Various single-cell RNA-seq methods used to generate libraries using a 1:1:1:1 mixture of four lymphocyte cell lines (Jurkat, TALL-104, EL4, IVA12).
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| Contributor(s) |
Yamawaki TM, Lu DR, Ellwanger DC, Bhatt D, Manzanillo P, Arias V, Zhou H, Yoon O, Homann O, Wang S, Li C |
| Citation(s) |
33472597 |
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| Submission date |
Dec 23, 2020 |
| Last update date |
Jan 27, 2021 |
| Contact name |
Tracy Yamawaki |
| E-mail(s) |
tyamawak@amgen.com
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| Organization name |
AMGEN, INC.
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| Street address |
1120 VETERANS BLVD.
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| City |
SOUTH SAN FRANCISCO |
| State/province |
California |
| ZIP/Postal code |
94080 |
| Country |
USA |
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| Platforms (1) |
| GPL24625 |
NextSeq 550 (Homo sapiens; Mus musculus) |
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| Samples (3) |
| GSM4987513 |
27_iCELL8_3pDE_lymphocyte_cell line_mix |
| GSM4987514 |
28_iCELL8_3pDE_lymphocyte_cell line_mix |
| GSM4987515 |
29_iCELL8_3pDEUMI_lymphocyte_cell line_mix |
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| This SubSeries is part of SuperSeries: |
| GSE163793 |
Systematic comparison of high-throughput single-cell RNA-seq methods for immune cell profiling |
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| Relations |
| BioProject |
PRJNA687537 |
| SRA |
SRP299143 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE163792_RAW.tar |
22.3 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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