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| Status |
Public on Jan 15, 2021 |
| Title |
Integrated analysis of multimodal single-cell data |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Other
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| Summary |
The simultaneous measurement of multiple modalities, known as multimodal analysis, represents an exciting frontier for single-cell genomics and necessitates new computational methods that can define cellular states based on multiple data types. Here, we introduce ‘weighted-nearest neighbor’ analysis, an unsupervised framework to learn the relative utility of each data type in each cell, enabling an integrative analysis of multiple modalities. We apply our procedure to a CITE-seq dataset of hundreds of thousands of human white blood cells alongside a panel of 228 antibodies to construct a multimodal reference atlas of the circulating immune system. We demonstrate that integrative analysis substantially improves our ability to resolve cell states and validate the presence of previously unreported lymphoid subpopulations. Moreover, we demonstrate how to leverage this reference to rapidly map new datasets, and to interpret immune responses to vaccination and COVID-19. Our approach represents a broadly applicable strategy to analyze single-cell multimodal datasets, including paired measurements of RNA and chromatin state, and to look beyond the transcriptome towards a unified and multimodal definition of cellular identity.
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| Overall design |
Human PBMCs were profiled using CITE-seq and cell hashing
*** Raw data will be deposited in dbGaP due to patient privacy concerns ***
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| Web link |
https://www.biorxiv.org/content/10.1101/2020.10.12.335331v1
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| Contributor(s) |
Hao Y |
| Citation(s) |
34062119 |
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| Submission date |
Jan 07, 2021 |
| Last update date |
Jul 08, 2021 |
| Contact name |
Yuhan Hao |
| E-mail(s) |
yhao@nygenome.org
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| Organization name |
New York Genome Center
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| Street address |
101 6th Ave
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| City |
New York |
| ZIP/Postal code |
10013 |
| Country |
USA |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (9)
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| Relations |
| BioProject |
PRJNA690251 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE164378_Antibody_HTO_info.xlsx |
30.7 Kb |
(ftp)(http) |
XLSX |
| GSE164378_RAW.tar |
1.4 Gb |
(http)(custom) |
TAR (of CSV, MTX, TSV) |
| GSE164378_sc.meta.data_3P.csv.gz |
3.0 Mb |
(ftp)(http) |
CSV |
| GSE164378_sc.meta.data_5P.csv.gz |
842.2 Kb |
(ftp)(http) |
CSV |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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