The Comparison of Two Single-cell Sequencing Platforms: BD Rhapsody and 10x Genomics Chromium

Gao, Caixia; Zhang, Mingnan; Chen, Lei

doi:10.2174/1389202921999200625220812

Cited by 66 publications

(60 citation statements)

References 36 publications

(41 reference statements)

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“…Other systems rely on single-cell isolation with magnetic beads in microwells, where individual cells are lysed and the beads are retrieved (BD Rhapsody) for targeted gene expression analysis. This method and other scRNA-seq methods have been discussed previously 111 , 112 .…”

Section: Single-cell Transcriptomicsmentioning

confidence: 99%

Immune cell profiling in atherosclerosis: role in research and precision medicine

Fernandez

Giannarelli

2021

Nat Rev Cardiol

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Inflammation is intimately involved at all stages of atherosclerosis and remains a substantial residual cardiovascular risk factor in optimally treated patients. The proof of concept that targeting inflammation reduces cardiovascular events in patients with a history of myocardial infarction has highlighted the urgent need to identify new immunotherapies to treat patients with atherosclerotic cardiovascular disease. Importantly, emerging data from new clinical trials show that successful immunotherapies for atherosclerosis need to be tailored to the specific immune alterations in distinct groups of patients. In this Review, we discuss how single-cell technologies -such as single-cell mass cytometry, single-cell RNA sequencing and cellular indexing of transcriptomes and epitopes by sequencing -are ideal for mapping the cellular and molecular composition of human atherosclerotic plaques and how these data can aid in the discovery of new precise immunotherapies. We also argue that single-cell data from studies in humans need to be rigorously validated in relevant experimental models, including rapidly emerging single-cell CRISPR screening technologies and mouse models of atherosclerosis. Finally, we discuss the importance of implementing single-cell immune monitoring tools in early phases of drug development to aid in the precise selection of the target patient population for data-driven translation into randomized clinical trials and the successful translation of new immunotherapies into the clinic.

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Section: Single-cell Transcriptomicsmentioning

confidence: 99%

Immune cell profiling in atherosclerosis: role in research and precision medicine

Fernandez

Giannarelli

2021

Nat Rev Cardiol

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“…We developed a custom qtSEQ strategy to quantify changes in the transcriptional program of individually sorted and indexed members of these rare lymphocyte sub-populations. High-fidelity cell purification is directly coupled to sensitive and targeted cDNA library formation to provide ~10-fold increased detection per single cell of targeted mRNA species compared to global strategies (Fan et al, 2015;Gao et al, 2020;Milpied et al, 2018;Peng et al, 2021;Wu et al, 2014). PCs have been difficult to sequence due to over-abundance of Ig mRNA signals per PC impacting resolution of gene expression studies (Higgins et al, 2019;Nutt et al, 2015).…”

Section: Discussionmentioning

confidence: 99%

PD-1 checkpoint blockade disrupts CD4 T cell regulated adaptive B cell tolerance to foreign antigens

Shuparski

et al. 2021

Preprint

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Adaptive B cell immunity to environmental antigens must be regulated by multiple CD4 T cell dependent tolerance mechanisms. Using integrated single cell strategies, we demonstrate that acute PD-1 blockade induces extensive and selective local anti-inflammatory IgG1 plasma cell (PC) differentiation. Expansion of pre-existing IgG1 germinal center (GC) B cell and enhanced GC programming without memory B cell involvement reveals an isotype-specific GC checkpoint that blocks steady-state IgG1 antibody maturation. While there was no adjuvant impact on immunization, acute PD-1 checkpoint blockade exaggerates anti-commensal IgG1 antibody production, alters microbiome composition and exerts its action in a CD4 T cell dependent manner. These findings reveal a PD-1 controlled adaptive B cell tolerance checkpoint that selectively constrains maturation of pre-existing anti-inflammatory antibodies to prevent over-reaction to steady-state foreign antigens.

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“…State-of-the-art scRNA-Seq analysis techniques can generate transcriptome information from thousands of cells. (Sasagawa et al, 2018(Sasagawa et al, , 2013Gao et al, 2020;Hayashi et al, 2018;Klein et al, 2015). Dimensional reduction of scRNA-Seq data provides a trajectory of cellular events and enables assignment of pseudo-time to each cell during differentiation and proliferation (Treutlein et al, 2014;Haghverdi et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Intracellular and intercellular gene regulatory networks inference from time-course individual RNA-Seq

Kashima

Shida

Yamashiro

et al. 2021

Preprint

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Motivation: Recent technical advances in bulk RNA-Seq have enabled time-course RNA-Seq of whole individual embryos to understand the underlying molecular mechanisms. Thus, we hypothesized that gene regulatory networks (GRNs) inferred from time-course individual RNA-Seq during embryonic development reveal intercellular regulatory relationships involved in signaling pathways. Results: Time-course bulk RNA-Seq of individual mouse embryos in early development, followed by pseudo-time analysis and GRN inference, demonstrated that GRN inference from RNA-Seq with pseudo-time can be applied for individual bulk RNA-Seq similar to scRNA-Seq. Validation using an experimental-source-based database showed that our approach could significantly infer GRN for all transcription factors in the database. Furthermore, the inferred ligand-related and receptor-related downstream genes were significantly overlapped. Overall, the inferred GRN include intracellular as well as intercellular regulatory relationships, which cannot be inferred from scRNA-Seq. Thus, inferring GRN from time-course bulk RNA-Seq is a novel approach for understanding the regulatory relationships underlying cellular events.

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The Comparison of Two Single-cell Sequencing Platforms: BD Rhapsody and 10x Genomics Chromium

Cited by 66 publications

References 36 publications

Immune cell profiling in atherosclerosis: role in research and precision medicine

Immune cell profiling in atherosclerosis: role in research and precision medicine

PD-1 checkpoint blockade disrupts CD4 T cell regulated adaptive B cell tolerance to foreign antigens

Intracellular and intercellular gene regulatory networks inference from time-course individual RNA-Seq

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