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Overview of single‐cell RNA sequencing analysis and its application to spermatogenesis research

Reproductive Medicine and Biology, 2023
Background Single‐cell transcriptomics allows parallel analysis of multiple cell types in tissues. Because testes comprise somatic cells and germ cells at various stages of spermatogenesis, single‐cell RNA sequencing is a powerful tool for investigating ...
Takahiro Suzuki
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Challenges and opportunities to computationally deconvolve heterogeneous tissue with varying cell sizes using single-cell RNA-sequencing datasets

Genome Biology, 2023
Deconvolution of cell mixtures in “bulk” transcriptomic samples from homogenate human tissue is important for understanding disease pathologies. However, several experimental and computational challenges impede transcriptomics-based deconvolution ...
Sean K. Maden, Sang Ho Kwon, Louise A. Huuki-Myers, Leonardo Collado-Torres, Stephanie C. Hicks, Kristen R. Maynard   +5 more
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Application of single-cell RNA sequencing technologies in aortic dilatation diseases [PDF]

Jichu yixue yu linchuang, 2022
Aortic dilation disease, represented by aortic dissection and aortic aneurysm, is the most dangerous disease in vascular surgery. The pathogenesis of this disease is not very clear.
ZHENG Kai, REN Hua-liang, ZHANG Wang-de, LI Chun-min
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Single-cell RNA Sequencing in Immunology

Current Genomics, 2020
The complex immune system is involved in multiple pathological processes. Single-cell RNA sequencing (scRNA-seq) is able to analyze complex cell mixtures correct to a single cell and single molecule, thus is qualified to analyze immune reactions in several diseases.
Yirui Cao, Yue Qiu, Guowei Tu, Cheng Yang   +3 more
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SMARTer single cell total RNA sequencing [PDF]

Nucleic Acids Research, 2019
Abstract Single cell RNA sequencing methods have been increasingly used to understand cellular heterogeneity. Nevertheless, most of these methods suffer from one or more limitations, such as focusing only on polyadenylated RNA, sequencing of only the 3′ end of the transcript, an exuberant fraction of reads mapping to ribosomal RNA ...
Karen Verboom, Celine Everaert, Nathalie Bolduc, Kenneth J Livak, Nurten Yigit, Dries Rombaut, Jasper Anckaert, Simon Lee, Morten T Venø, Jørgen Kjems, Frank Speleman, Pieter Mestdagh, Jo Vandesompele   +12 more
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Single Cell RNA Sequencing in Atherosclerosis Research [PDF]

Circulation Research, 2020
Technological advances in characterizing molecular heterogeneity at the single cell level have ushered in a deeper understanding of the biological diversity of cells present in tissues including atherosclerotic plaques. New subsets of cells have been discovered among cell types previously considered homogenous. The commercial availability of systems to
Jesse W. Williams, Holger Winkels, Christopher P. Durant, Konstantin Zaitsev, Yanal Ghosheh, Klaus Ley   +5 more
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Crafting a blueprint for single-cell RNA sequencing [PDF]

Trends in Plant Science, 2022
Droplet-based single-cell RNA sequencing (scRNA-Seq) has moved rapidly from a technology with great potential to a method applied to ever-broader questions. The detailed information that scRNA-Seq offers has proven incredibly powerful in resolving cell responses to developmental and environmental cues.
Tom Denyer, Marja C.P. Timmermans
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Experimental design for single-cell RNA sequencing [PDF]

Briefings in Functional Genomics, 2017
Single-cell RNA sequencing (scRNA-seq) has opened new avenues for the characterization of heterogeneity in a large variety of cellular systems. As this is a relatively new technique, the field is fast evolving. Here, we discuss general considerations in experimental design and the two most popular approaches, plate-based Smart-Seq2 and microdroplet ...
Baran-Gale, Jeanette, Chandra, Tamir, Kirschner, Kristina   +2 more
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Rapid and sensitive single-cell RNA sequencing with SHERRY2 [PDF]

BMC Biology, 2021
Abstract Background Prevalent single-cell transcriptomic profiling (scRNA-seq) methods are mainly based on the synthesis and enrichment of full-length double-stranded complementary DNA. These approaches are challenging to generate accurate quantification of transcripts when their abundance is ...
Lin Di, Bo Liu, Yuzhu Lyu, Shihui Zhao, Yuhong Pang, Chen Zhang, Jianbin Wang, Hai Qi, Jie Shen, Yanyi Huang   +9 more
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Glyoxal as alternative fixative for single cell RNA sequencing [PDF]

G3: Genes, Genomes, Genetics, 2021
Abstract Single cell RNA sequencing (scRNA-seq) has become an important method to identify cell types, delineate the trajectories of cell differentiation in whole organisms and understand the heterogeneity in cellular responses.
Josephine Bageritz, Niklas Krausse, Schayan Yousefian, Svenja Leible, Erica Valentini, Michael Boutros   +5 more
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