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Gupta K, Lalit M, Biswas A, Sanada CD, Greene C, Hukari K, Maulik U, Bandyopadhyay S, Ramalingam N, Ahuja G, Ghosh A, Sengupta D. Modeling expression ranks for noise-tolerant differential expression analysis of scRNA-seq data. Genome Res 2021; 31:689-697. [PMID: 33674351 PMCID: PMC8015842 DOI: 10.1101/gr.267070.120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 02/22/2021] [Indexed: 12/13/2022]
Abstract
Systematic delineation of complex biological systems is an ever-challenging and resource-intensive process. Single-cell transcriptomics allows us to study cell-to-cell variability in complex tissues at an unprecedented resolution. Accurate modeling of gene expression plays a critical role in the statistical determination of tissue-specific gene expression patterns. In the past few years, considerable efforts have been made to identify appropriate parametric models for single-cell expression data. The zero-inflated version of Poisson/negative binomial and log-normal distributions have emerged as the most popular alternatives owing to their ability to accommodate high dropout rates, as commonly observed in single-cell data. Although the majority of the parametric approaches directly model expression estimates, we explore the potential of modeling expression ranks, as robust surrogates for transcript abundance. Here we examined the performance of the discrete generalized beta distribution (DGBD) on real data and devised a Wald-type test for comparing gene expression across two phenotypically divergent groups of single cells. We performed a comprehensive assessment of the proposed method to understand its advantages compared with some of the existing best-practice approaches. We concluded that besides striking a reasonable balance between Type I and Type II errors, ROSeq, the proposed differential expression test, is exceptionally robust to expression noise and scales rapidly with increasing sample size. For wider dissemination and adoption of the method, we created an R package called ROSeq and made it available on the Bioconductor platform.
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Affiliation(s)
- Krishan Gupta
- Department of Computer Science and Engineering, Indraprastha Institute of Information Technology, Delhi 110020, India
| | - Manan Lalit
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany
| | - Aditya Biswas
- Microsoft India Private Limited, Hyderabad, Telangana 500032, India
| | - Chad D Sanada
- Fluidigm Corporation, South San Francisco, California 94080, USA
| | - Cassandra Greene
- Fluidigm Corporation, South San Francisco, California 94080, USA
| | - Kyle Hukari
- Fluidigm Corporation, South San Francisco, California 94080, USA
| | - Ujjwal Maulik
- Department of Computer Science, Jadavpur University, Kolkata, West Bengal 700032, India
| | | | | | - Gaurav Ahuja
- Department of Computational Biology, Indraprastha Institute of Information Technology, Delhi 110020, India
| | - Abhik Ghosh
- Interdisciplinary Statistical Research Unit, Indian Statistical Institute, Kolkata 700108, India
| | - Debarka Sengupta
- Department of Computer Science and Engineering, Indraprastha Institute of Information Technology, Delhi 110020, India.,Department of Computational Biology, Indraprastha Institute of Information Technology, Delhi 110020, India.,Centre for Artificial Intelligence, Indraprastha Institute of Information Technology, Delhi 110020, India.,Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD 4000, Australia
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Abstract
Single-cell functional analysis provides a natural next step in the now widely adopted single-cell mRNA sequencing studies. Functional studies can be designed to study cellular context by using single-cell culture, perturbation, manipulation, or treatment. Here we present a method for a functional study of 48 single cells by single-cell isolation, dosing, and mRNA sequencing with an integrated fluidic circuit (IFC) on the Fluidigm® Polaris™ system. The major procedures required to execute this protocol are (1) cell preparation and staining; (2) priming, single-cell selection, cell dosing, cell staining, and cDNA generation on the Polaris IFC; and (3) preparation and sequencing of single-cell mRNA-seq libraries. The cell preparation and staining steps employ the use of a universal tracking dye to trace all cells that enter the IFC, while additional fluorescence dyes chosen by the user can be used to differentiate cell types in the overall mix. The steps on the Polaris IFC follow standard protocols, which are also described in the Fluidigm user documentation. The library preparation step adds Illumina® Nextera® XT indexes to the cDNA generated on the Polaris IFC. The resulting sequencing libraries can be sequenced on any Illumina sequencing platform.
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Affiliation(s)
| | - Aik T Ooi
- Fluidigm Corporation, South San Francisco, CA, USA
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Ramalingam N, Fowler B, Szpankowski L, Leyrat AA, Hukari K, Maung MT, Yorza W, Norris M, Cesar C, Shuga J, Gonzales ML, Sanada CD, Wang X, Yeung R, Hwang W, Axsom J, Devaraju NSGK, Angeles ND, Greene C, Zhou MF, Ong ES, Poh CC, Lam M, Choi H, Htoo Z, Lee L, Chin CS, Shen ZW, Lu CT, Holcomb I, Ooi A, Stolarczyk C, Shuga T, Livak KJ, Larsen C, Unger M, West JAA. Corrigendum: Fluidic Logic Used in a Systems Approach to Enable Integrated Single-Cell Functional Analysis. Front Bioeng Biotechnol 2017; 5:11. [PMID: 28299310 PMCID: PMC5349287 DOI: 10.3389/fbioe.2017.00011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Accepted: 02/06/2017] [Indexed: 11/19/2022] Open
Affiliation(s)
- Naveen Ramalingam
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Brian Fowler
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Lukasz Szpankowski
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Anne A Leyrat
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Kyle Hukari
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Myo Thu Maung
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Wiganda Yorza
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Michael Norris
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Chris Cesar
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Joe Shuga
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Michael L Gonzales
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Chad D Sanada
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Xiaohui Wang
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Rudy Yeung
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Win Hwang
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Justin Axsom
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | | | - Ninez Delos Angeles
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Cassandra Greene
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Ming-Fang Zhou
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Eng-Seng Ong
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Chang-Chee Poh
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Marcos Lam
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Henry Choi
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Zaw Htoo
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Leo Lee
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Chee-Sing Chin
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Zhong-Wei Shen
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Chong T Lu
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Ilona Holcomb
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Aik Ooi
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Craig Stolarczyk
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Tony Shuga
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Kenneth J Livak
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Cate Larsen
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Marc Unger
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Jay A A West
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
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Ramalingam N, Fowler B, Szpankowski L, Leyrat AA, Hukari K, Maung MT, Yorza W, Norris M, Cesar C, Shuga J, Gonzales ML, Sanada CD, Wang X, Yeung R, Hwang W, Axsom J, Devaraju NSGK, Angeles ND, Greene C, Zhou MF, Ong ES, Poh CC, Lam M, Choi H, Htoo Z, Lee L, Chin CS, Shen ZW, Lu CT, Holcomb I, Ooi A, Stolarczyk C, Shuga T, Livak KJ, Larsen C, Unger M, West JAA. Fluidic Logic Used in a Systems Approach to Enable Integrated Single-Cell Functional Analysis. Front Bioeng Biotechnol 2016; 4:70. [PMID: 27709111 PMCID: PMC5030342 DOI: 10.3389/fbioe.2016.00070] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 08/23/2016] [Indexed: 12/18/2022] Open
Abstract
The study of single cells has evolved over the past several years to include expression and genomic analysis of an increasing number of single cells. Several studies have demonstrated wide spread variation and heterogeneity within cell populations of similar phenotype. While the characterization of these populations will likely set the foundation for our understanding of genomic- and expression-based diversity, it will not be able to link the functional differences of a single cell to its underlying genomic structure and activity. Currently, it is difficult to perturb single cells in a controlled environment, monitor and measure the response due to perturbation, and link these response measurements to downstream genomic and transcriptomic analysis. In order to address this challenge, we developed a platform to integrate and miniaturize many of the experimental steps required to study single-cell function. The heart of this platform is an elastomer-based integrated fluidic circuit that uses fluidic logic to select and sequester specific single cells based on a phenotypic trait for downstream experimentation. Experiments with sequestered cells that have been performed include on-chip culture, exposure to various stimulants, and post-exposure image-based response analysis, followed by preparation of the mRNA transcriptome for massively parallel sequencing analysis. The flexible system embodies experimental design and execution that enable routine functional studies of single cells.
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Affiliation(s)
- Naveen Ramalingam
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Brian Fowler
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Lukasz Szpankowski
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Anne A Leyrat
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Kyle Hukari
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Myo Thu Maung
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Wiganda Yorza
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Michael Norris
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Chris Cesar
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Joe Shuga
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Michael L Gonzales
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Chad D Sanada
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Xiaohui Wang
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Rudy Yeung
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Win Hwang
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Justin Axsom
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | | | - Ninez Delos Angeles
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Cassandra Greene
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Ming-Fang Zhou
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Eng-Seng Ong
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Chang-Chee Poh
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Marcos Lam
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Henry Choi
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Zaw Htoo
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Leo Lee
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Chee-Sing Chin
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Zhong-Wei Shen
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Chong T Lu
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Ilona Holcomb
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Aik Ooi
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Craig Stolarczyk
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Tony Shuga
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Kenneth J Livak
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Cate Larsen
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Marc Unger
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
| | - Jay A A West
- New Technologies Research Department, Fluidigm Corporation , South San Francisco, CA , USA
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