Single-Cell RNA Sequencing Analysis Using Fluidigm C1 Platform for Characterization of Heterogeneous Transcriptomes

doi:10.1007/978-1-0716-2376-3_19

. 2022:2508:261-278.

doi: 10.1007/978-1-0716-2376-3_19.

Single-Cell RNA Sequencing Analysis Using Fluidigm C1 Platform for Characterization of Heterogeneous Transcriptomes

Jinhong Kim¹, Paola A Marignani^{2

3}

Affiliations

¹ Department of Biochemistry and Molecular Biology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada.
² Department of Biochemistry and Molecular Biology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada. paola.marignani@dal.ca.
³ Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada. paola.marignani@dal.ca.

PMID: 35737246
DOI: 10.1007/978-1-0716-2376-3_19

Single-Cell RNA Sequencing Analysis Using Fluidigm C1 Platform for Characterization of Heterogeneous Transcriptomes

Jinhong Kim et al. Methods Mol Biol. 2022.

. 2022:2508:261-278.

doi: 10.1007/978-1-0716-2376-3_19.

Authors

Jinhong Kim¹, Paola A Marignani^{2

3}

Affiliations

¹ Department of Biochemistry and Molecular Biology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada.
² Department of Biochemistry and Molecular Biology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada. paola.marignani@dal.ca.
³ Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada. paola.marignani@dal.ca.

PMID: 35737246
DOI: 10.1007/978-1-0716-2376-3_19

Abstract

Single-cell RNA sequencing (scRNA-seq) is an innovative technology that can be used to characterize transcriptome heterogeneity at the single-cell resolution. The Fluidigm C1 is an automated system for preparing complementary deoxyribonucleic acid (cDNA) samples that have been synthesized and preamplified from single cells for next-generation sequencing (NGS) analysis. Herein, we detail a workflow and protocol for scRNA-seq analysis of 3'-end enriched cDNA libraries and introduce strategies for validation of differential gene expression.

Keywords: Differential gene expression; Fluidigm C1 systems; Protein expression analysis; Validation; qRT-PCR; scRNA-seq.

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References

1. Choi YH, Kim JK (2019) Dissecting cellular heterogeneity using single-cell RNA sequencing. Mol Cells 42(3):189–199 - PubMed - PMC
1. Valdes-Mora F, Handler K, Law AMK, Salomon R, Oakes SR, Ormandy CJ, Gallego-Ortega D (2018) Single-cell transcriptomics in cancer immunobiology: the future of precision oncology. Front Immunol 9(2582):1–30
1. Sharma A, Cao EY, Kumar V, Zhang X, Leong HS, Wong AML, Ramakrishnan N, Hakimullah M, Teo HMV, Chong FT, Chia S, Thangavelu MT, Kwang XL, Gupta R, Clark JR, Periyasamy G, Iyer NG, DasGupta R (2018) Longitudinal single-cell RNA sequencing of patient-derivedprimary cells reveals drug-induced infidelity in stem cell hierarchy. Nat Commun 9(1):4931 - DOI
1. Kim J-H, Xu Z, Marignani PA (2021) Identifying unique markers of lung cancer using single-cell RNA sequencing. NPJ Genom Med. 15:6(1):87
1. Kim D, Langmead B, Salzberg SL (2015) HISAT: a fast spliced aligner with low memory requirements. Nat Methods 12(4):357–360 - DOI

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[1] Choi YH, Kim JK (2019) Dissecting cellular heterogeneity using single-cell RNA sequencing. Mol Cells 42(3):189–199 - PubMed - PMC

[2] Choi YH, Kim JK (2019) Dissecting cellular heterogeneity using single-cell RNA sequencing. Mol Cells 42(3):189–199 - PubMed - PMC

[3] Valdes-Mora F, Handler K, Law AMK, Salomon R, Oakes SR, Ormandy CJ, Gallego-Ortega D (2018) Single-cell transcriptomics in cancer immunobiology: the future of precision oncology. Front Immunol 9(2582):1–30

[4] Valdes-Mora F, Handler K, Law AMK, Salomon R, Oakes SR, Ormandy CJ, Gallego-Ortega D (2018) Single-cell transcriptomics in cancer immunobiology: the future of precision oncology. Front Immunol 9(2582):1–30

[5] Sharma A, Cao EY, Kumar V, Zhang X, Leong HS, Wong AML, Ramakrishnan N, Hakimullah M, Teo HMV, Chong FT, Chia S, Thangavelu MT, Kwang XL, Gupta R, Clark JR, Periyasamy G, Iyer NG, DasGupta R (2018) Longitudinal single-cell RNA sequencing of patient-derivedprimary cells reveals drug-induced infidelity in stem cell hierarchy. Nat Commun 9(1):4931 - DOI

[6] Sharma A, Cao EY, Kumar V, Zhang X, Leong HS, Wong AML, Ramakrishnan N, Hakimullah M, Teo HMV, Chong FT, Chia S, Thangavelu MT, Kwang XL, Gupta R, Clark JR, Periyasamy G, Iyer NG, DasGupta R (2018) Longitudinal single-cell RNA sequencing of patient-derivedprimary cells reveals drug-induced infidelity in stem cell hierarchy. Nat Commun 9(1):4931 - DOI

[7] Kim J-H, Xu Z, Marignani PA (2021) Identifying unique markers of lung cancer using single-cell RNA sequencing. NPJ Genom Med. 15:6(1):87

[8] Kim J-H, Xu Z, Marignani PA (2021) Identifying unique markers of lung cancer using single-cell RNA sequencing. NPJ Genom Med. 15:6(1):87

[9] Kim D, Langmead B, Salzberg SL (2015) HISAT: a fast spliced aligner with low memory requirements. Nat Methods 12(4):357–360 - DOI

[10] Kim D, Langmead B, Salzberg SL (2015) HISAT: a fast spliced aligner with low memory requirements. Nat Methods 12(4):357–360 - DOI

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Single-Cell RNA Sequencing Analysis Using Fluidigm C1 Platform for Characterization of Heterogeneous Transcriptomes

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Single-Cell RNA Sequencing Analysis Using Fluidigm C1 Platform for Characterization of Heterogeneous Transcriptomes

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