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A hybrid demultiplexing strategy that improves performance and robustness of cell hashing.
Brief Bioinform
May 2024
Gale and Ira Drukier Institute for Children's Health, Weill Cornell Medicine, 413 E. 69th Street, New York, NY 10021, United States.
Cell hashing, a nucleotide barcode-based method that allows users to pool multiple samples and demultiplex in downstream analysis, has gained widespread popularity in single-cell sequencing due to its compatibility, simplicity, and cost-effectiveness. Despite these advantages, the performance of this method remains unsatisfactory under certain circumstances, especially in experiments that have imbalanced sample sizes or use many hashtag antibodies. Here, we introduce a hybrid demultiplexing strategy that increases accuracy and cell recovery in multi-sample single-cell experiments.
View Article and Find Full Text PDFA hybrid demultiplexing strategy that improves performance and robustness of cell hashing.
bioRxiv
November 2023
Gale and Ira Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY, 10065, USA.
Recent advances in single cell RNA sequencing allow users to pool multiple samples and demultiplex in downstream analysis, which greatly increase experimental efficiency and cost-effectiveness. Among all the demultiplexing methods, nucleotide barcode-based cell hashing has gained widespread popularity due to its compatibility and simplicity. Despite these advantages, certain issues of this technic remain to be solved, such as challenges in distinguishing true positive from background, high reagent cost for samples with large cell numbers, and unpredictable false negative and false doublet rates.
View Article and Find Full Text PDFWho polarizes Twitter? Ideological polarization, partisan groups and strategic networked campaigning on Twitter during the 2017 and 2021 German Federal elections 'Bundestagswahlen'.
Soc Netw Anal Min
October 2022
Center for Digital Governance, Hertie School, Berlin, Germany.
Political campaign activities are increasingly digital. A crucial part of digital campaigning is communication efforts on social media platforms. As a forum for political discourse and political communication, parties and candidates on Twitter share public messages and aim to attract media attention and persuade voters.
View Article and Find Full Text PDFUniversal Surface Biotinylation: a simple, versatile and cost-effective sample multiplexing method for single-cell RNA-seq analysis.
DNA Res
May 2022
Technology and Development Team for Mammalian Genome Dynamics, RIKEN BioResource Research Center, Tsukuba City, Ibaraki 305-0074, Japan.
Recent advances in single-cell analysis technology have made it possible to analyse tens of thousands of cells at a time. In addition, sample multiplexing techniques, which allow the analysis of several types of samples in a single run, are very useful for reducing experimental costs and improving experimental accuracy. However, a problem with this technique is that antigens and antibodies for universal labelling of various cell types may not be fully available.
View Article and Find Full Text PDFGenotype-free demultiplexing of pooled single-cell RNA-seq.
Genome Biol
December 2019
Genome Innovation Hub, The University of Queensland, 306 Carmody Road, St Lucia, Brisbane, QLD 4072, Australia.
A variety of methods have been developed to demultiplex pooled samples in a single cell RNA sequencing (scRNA-seq) experiment which either require hashtag barcodes or sample genotypes prior to pooling. We introduce scSplit which utilizes genetic differences inferred from scRNA-seq data alone to demultiplex pooled samples. scSplit also enables mapping clusters to original samples.
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