Dataset Information

Palladium-based mass tag cell barcoding with a doublet-filtering scheme and single-cell deconvolution algorithm.

ABSTRACT: Mass-tag cell barcoding (MCB) labels individual cell samples with unique combinatorial barcodes, after which they are pooled for processing and measurement as a single multiplexed sample. The MCB method eliminates variability between samples in antibody staining and instrument sensitivity, reduces antibody consumption and shortens instrument measurement time. Here we present an optimized MCB protocol. The use of palladium-based labeling reagents expands the number of measurement channels available for mass cytometry and reduces interference with lanthanide-based antibody measurement. An error-detecting combinatorial barcoding scheme allows cell doublets to be identified and removed from the analysis. A debarcoding algorithm that is single cell-based rather than population-based improves the accuracy and efficiency of sample deconvolution. This debarcoding algorithm has been packaged into software that allows rapid and unbiased sample deconvolution. The MCB procedure takes 3-4 h, not including sample acquisition time of ∼1 h per million cells.

SUBMITTER: Zunder ER

PROVIDER: S-EPMC4347881 | biostudies-literature | 2015 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Palladium-based mass tag cell barcoding with a doublet-filtering scheme and single-cell deconvolution algorithm.

Zunder Eli R ER Finck Rachel R Behbehani Gregory K GK Amir El-Ad D el-AD Krishnaswamy Smita S Gonzalez Veronica D VD Lorang Cynthia G CG Bjornson Zach Z Spitzer Matthew H MH Bodenmiller Bernd B Fantl Wendy J WJ Pe'er Dana D Nolan Garry P GP

Nature protocols 20150122 2

Mass-tag cell barcoding (MCB) labels individual cell samples with unique combinatorial barcodes, after which they are pooled for processing and measurement as a single multiplexed sample. The MCB method eliminates variability between samples in antibody staining and instrument sensitivity, reduces antibody consumption and shortens instrument measurement time. Here we present an optimized MCB protocol. The use of palladium-based labeling reagents expands the number of measurement channels availab ...[more]

PMID: 25612231

Similar Datasets

Project description:Doublets are a key confounding factor in the analysis of scRNA-seq data, as they can interfere with differential expression analysis and disrupt developmental trajectories. However, due to the randomness of the algorithms, most doublet removal methods still leave a certain proportion of doublets after application. In this study, we proposed a multi-round doublet removal (MRDR) strategy, that ran the algorithm in cycles multiple times to effectively reduce randomness while enhancing the effectiveness of doublet removal. We evaluated the MRDR strategy in 14 real-world datasets, 29 barcoded scRNA-seq datasets, and 106 synthetic datasets with four popular doublet detection tools, including DoubletFinder, cxds, bcds, and hybrid. We found that in real-world datasets, the DoubletFinder had a better performance in MRDR strategy compared to a single removal of doublets and the recall rate improved by 50 % for two rounds of doublet removal compared to one round, and the performance of the other three doublet algorithms improved the ROC by about 0.04. In barcoded scRNA-seq datasets, we found that using cxds for two rounds of doublet removal yielded the best results. Subsequently, in simulated datasets, we proved that the multi-round removal strategy was more effective in removing doublets than a single removal, with cxds showing the best results when applied twice, and the ROC of the four methods during the two rounds of removal improved by at least 0.05 compared to single removal. Finally, compared to running the algorithm once, we found that the MRDR strategy was more beneficial for differential gene expression analysis and cell trajectory inference when using default analysis parameters. Overall, we proved that the MRDR strategy was more effective in removing doublets and advantageous for downstream analyses, and the strategy could be incorporated into the standard analysis pipeline for scRNA-seq experiments and recommend using cxds to remove doublets through two rounds of algorithm iteration.

Dataset Information

Palladium-based mass tag cell barcoding with a doublet-filtering scheme and single-cell deconvolution algorithm.

Publications

Palladium-based mass tag cell barcoding with a doublet-filtering scheme and single-cell deconvolution algorithm.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets