scholarly journals The Trends of Single-Cell Analysis: A Global Study

2020 ◽  
Vol 2020 ◽  
pp. 1-10
Author(s):  
Hua Tian ◽  
Haifeng Liu ◽  
Yuanyuan Zhu ◽  
Dan Xing ◽  
Bin Wang
Keyword(s):  
Single Cell ◽  
Single Cell Analysis ◽  
Bibliographic Coupling ◽  
In Vivo Studies ◽  
Cell Analysis ◽  
The Usa ◽  
Visualization Of Data ◽  
Number Of Publications

Objective. The field of single-cell analysis has rapidly grown worldwide, and a bibliometric analysis and visualization of data and publications pertaining to such single-cell research has the potential to offer insights into the development of this field over the past two decades while also highlighting future avenues of research. Methods. Single-cell analysis-related studies published from 2000-2019 were identified through searches of the Web of Science, Scopus, and PubMed databases, and corresponding bibliometric data were systematically compiled. Extracted data from each study included author names, country of origin, and affiliations. GraphPad Prism was used to analyze these data, while VOSviewer was used to perform global analyses of bibliographic coupling, coauthorship, cocitation, and co-occurrence. Results. In total, 4,071 relevant studies were included in this analysis. The number of publications increased substantially with time, suggesting that single-cell analyses are becoming increasingly more prevalent in recent years. Studies from the USA had the greatest impact in this field, with higher H -index values and numbers of citations relative to other countries, whereas Israel exhibited the highest average number of citations per publication. Bibliographic coupling, coauthorship, cocitation, and co-occurrence analyses revealed that Analytical Chemistry was associated with the highest number of publications in this field, and the University of Stanford contributed the most to this field. The most cited study included in this analysis was published by Macosko et al. in 2015 in Cell. Co-occurrence analyses revealed that the most common single-cell research topics included “mechanistic studies,” “in vitro studies,” “in vivo studies,” and “fabrication studies.” Conclusions. Single-cell analyses are a rapidly growing area of scientific interest, and higher volumes of publications in this field are expected in the coming years, particularly for studies conducting fabrication and in vivo single-cell analyses.

scholarly journals Single Cell Analysis Reveals That IL-4 Receptor/Stat6 Signaling Is Not Required for the In Vivo or In Vitro Development of CD4+Lymphocytes with a Th2 Cytokine Profile

2000 ◽  
Vol 164 (6) ◽  
pp. 3047-3055 ◽  
Author(s):  
Dragana Jankovic ◽  
Marika C. Kullberg ◽  
Nancy Noben-Trauth ◽  
Patricia Caspar ◽  
William E. Paul ◽  
...  
Keyword(s):  
Single Cell ◽  
Single Cell Analysis ◽  
Cytokine Profile ◽  
Cell Analysis ◽  
In Vitro Development ◽  
Th2 Cytokine ◽  
Vitro Development ◽  
Cd4 Lymphocytes

scholarly journals Single-cell analysis reveals a nestin+ tendon stem/progenitor cell population with strong tenogenic potentiality

2016 ◽  
Vol 2 (11) ◽  
pp. e1600874 ◽  
Author(s):  
Zi Yin ◽  
Jia-jie Hu ◽  
Long Yang ◽  
Ze-Feng Zheng ◽  
Cheng-rui An ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Cell Population ◽  
Single Cell Analysis ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Cell Analysis ◽  
Nestin Expression

The repair of injured tendons remains a formidable clinical challenge because of our limited understanding of tendon stem cells and the regulation of tenogenesis. With single-cell analysis to characterize the gene expression profiles of individual cells isolated from tendon tissue, a subpopulation of nestin+ tendon stem/progenitor cells (TSPCs) was identified within the tendon cell population. Using Gene Expression Omnibus datasets and immunofluorescence assays, we found that nestin expression was activated at specific stages of tendon development. Moreover, isolated nestin+ TSPCs exhibited superior tenogenic capacity compared to nestin− TSPCs. Knockdown of nestin expression in TSPCs suppressed their clonogenic capacity and reduced their tenogenic potential significantly both in vitro and in vivo. Hence, these findings provide new insights into the identification of subpopulations of TSPCs and illustrate the crucial roles of nestin in TSPC fate decisions and phenotype maintenance, which may assist in future therapeutic strategies to treat tendon disease.

scholarly journals Assessing the Heterogeneity of Cardiac Non-myocytes and the Effect of Cell Culture with Integrative Single Cell Analysis

2020 ◽  
Author(s):  
Brian S. Iskra ◽  
Logan Davis ◽  
Henry E. Miller ◽  
Yu-Chiao Chiu ◽  
Alexander R. Bishop ◽  
...  
Keyword(s):  
Cell Culture ◽  
Single Cell ◽  
Single Cell Analysis ◽  
Cell Types ◽  
Cell Analysis ◽  
Mass Cytometry ◽  
Single Cell Rna Sequencing ◽  
High Depth

AbstractCardiac non-myocytes comprise a diverse and crucial cell population in the heart that plays dynamic roles in cardiac wound healing and growth. Non-myocytes broadly fall into four cell types: endothelium, fibroblasts, leukocytes, and pericytes. Here we characterize the diversity of the non-myocytes in vivo and in vitro using mass cytometry. By leveraging single-cell RNA sequencing we inform the design of a mass cytometry panel. To aid in annotation of the mass cytometry datasets, we utilize data integration with a neural network. We introduce approximately 460,000∼ single cell proteomes of non-myocytes as well as 5,000∼ CD31 negative single cell transcriptomes. Using our data, as well as previously reported datasets, we characterize cardiac non-myocytes with high depth in six mice, characterizing novel surface markers (CD9, CD200, Notch3, and FolR2). Further, we find that extended cell culture promotes the proliferation of CD45+CD11b+FolR2+IAIE- myeloid cells in addition to fibroblasts.

Fabrication of high-aspect-ratio microstructures in polymer microfluid chips for in vitro single-cell analysis

2016 ◽  
Vol 61 (10) ◽  
pp. 1566-1571 ◽  
Author(s):  
A. S. Bukatin ◽  
I. S. Mukhin ◽  
E. I. Malyshev ◽  
I. V. Kukhtevich ◽  
A. A. Evstrapov ◽  
...  
Keyword(s):  
Aspect Ratio ◽  
Single Cell ◽  
High Aspect Ratio ◽  
Single Cell Analysis ◽  
Cell Analysis

scholarly journals P-165 Cytometry-Based Single Cell Analysis of Intact Epithelial Signaling Reveals MAPK Activation Divergent from TNF-α-Induced Apoptosis in Vivo

2016 ◽  
Vol 22 ◽  
pp. S59-S60
Author(s):  
Alan Simmons ◽  
Amrita Banerjee ◽  
Eliot McKinley ◽  
Cherieʼ Scurrah ◽  
Jeffrey Franklin ◽  
...  
Keyword(s):  
Single Cell ◽  
Single Cell Analysis ◽  
Cell Analysis ◽  
Mapk Activation ◽  
Tnf Α ◽  
Induced Apoptosis

scholarly journals Single-cell analysis reveals IGF-1 potentiation of inhibition of the TGF-β/Smad pathway of fibrosis in human keratocytes in vitro

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Tomislav Sarenac ◽  
Martin Trapecar ◽  
Lidija Gradisnik ◽  
Marjan Slak Rupnik ◽  
Dusica Pahor
Keyword(s):  
Single Cell ◽  
Single Cell Analysis ◽  
Cell Analysis ◽  
Smad Pathway ◽  
Human Keratocytes

scholarly journals HIV-1 provirus transcription and translation in macrophages differs from pre-integrated cDNA complexes and requires E2F transcriptional programs

2021 ◽  
Author(s):  
Albebson L. Lim ◽  
Philip Moos ◽  
Christopher D. Pond ◽  
Erica C. Larson ◽  
Laura J. Martins ◽  
...  
Keyword(s):  
Single Cell ◽  
Single Cell Analysis ◽  
Immunological Response ◽  
Virus Production ◽  
Cell Analysis ◽  
Gene Transcripts ◽  
Nuanced Understanding ◽  
New Perspective ◽  
Hiv 1

AbstractHIV-1 cDNA pre-integration complexes have been shown to persist for weeks in macrophages and to be transcriptionally active. Early and late gene transcripts are produced, along with some viral proteins, yet whole virus is not. While previous work has focused on the transcription and translation of HIV-1 genes; our understanding of cellular milieu that accompanies viral production is incomplete. We have used an in vitro system to model HIV-1 infection of macrophages, and single cell RNA sequencing (scRNA-seq) to compare the transcriptomes of uninfected cells, cells harboring pre-integration HIV-1 complexes (PIC) and those containing integrated provirus and actively making late HIV proteins. These are also compared to control cells, not exposed to virus.Several observations provide new perspective on the effects of HIV-1 transcription from pre-integrated cDNA versus from integrated provirus. First, HIV-1 transcript levels do not necessarily correlate with virus production, cells harboring PIC cDNA have transcript loads comparable to cells transcribing from provirus and making p24, mCherry, and vpu proteins. Second, all HIV-1 transcripts are easily detectable in abundance from PIC cDNA transcription, as is the case with cells transcribing from provirus, although the frequency of PIC cells with detectable gag-pol, tat, env, and nef transcripts is higher than the corresponding frequencies observed for “Provirus cells”. Third, the background transcriptomes of cells harboring pre- integrated HIV-1 cDNA are not otherwise detectably altered from cells not containing any HIV- 1 transcript. Fourth, integration and production of p24, mCherry, and Vpu proteins is accompanied by a switch from transcriptomes characterized by NFkB and AP-1 promoted transcription to a transcriptome characterized by E2F family transcription products. While some of these observations may seem heretical, single cell analysis provides a more nuanced understanding of PIC cDNA transcription and the transcriptomic changes that support HIV-1 protein production from integrated provirus.Author SummarySingle cell analysis is able to distinguish between HIV-1 infected macrophage cells that are transcribing pre-integrated HIV-1 cDNA and those transcribing HIV-1 provirus. Only cells transcribing HIV-1 provirus are making p24, marker mCherry and Vpu proteins, which corresponds with a change in the host cell’s background transcriptome from one expressing viral restriction and immunological response genes to one that is expressing genes associated with cell replication and oxidative phosphorylation.

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