scholarly journals Single-Cell Transcriptome Analysis as a Promising Tool to Study Pluripotent Stem Cell Reprogramming

2021 ◽  
Vol 22 (11) ◽  
pp. 5988
Author(s):  
Hyun Kyu Kim ◽  
Tae Won Ha ◽  
Man Ryul Lee
Keyword(s):  
Stem Cells ◽  
Single Cell ◽  
Cell Fate ◽  
Human Cell ◽  
Transcriptome Analysis ◽  
Single Cell Analysis ◽  
Embryonic Stem ◽  
Single Cell Level ◽  
Cell Analysis ◽  
Cell Level

Cells are the basic units of all organisms and are involved in all vital activities, such as proliferation, differentiation, senescence, and apoptosis. A human body consists of more than 30 trillion cells generated through repeated division and differentiation from a single-cell fertilized egg in a highly organized programmatic fashion. Since the recent formation of the Human Cell Atlas consortium, establishing the Human Cell Atlas at the single-cell level has been an ongoing activity with the goal of understanding the mechanisms underlying diseases and vital cellular activities at the level of the single cell. In particular, transcriptome analysis of embryonic stem cells at the single-cell level is of great importance, as these cells are responsible for determining cell fate. Here, we review single-cell analysis techniques that have been actively used in recent years, introduce the single-cell analysis studies currently in progress in pluripotent stem cells and reprogramming, and forecast future studies.

scholarly journals Microfluidic Single-Cell Manipulation and Analysis: Methods and Applications

Micromachines ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 104 ◽  
Author(s):  
Tao Luo ◽  
Lei Fan ◽  
Rong Zhu ◽  
Dong Sun
Keyword(s):  
Single Cell ◽  
Single Cell Analysis ◽  
Single Cells ◽  
Petri Dish ◽  
Cell Manipulation ◽  
Single Cell Level ◽  
Cell Analysis ◽  
Cell Level ◽  
Advantages And Disadvantages ◽  
Single Cell Manipulation

In a forest of a hundred thousand trees, no two leaves are alike. Similarly, no two cells in a genetically identical group are the same. This heterogeneity at the single-cell level has been recognized to be vital for the correct interpretation of diagnostic and therapeutic results of diseases, but has been masked for a long time by studying average responses from a population. To comprehensively understand cell heterogeneity, diverse manipulation and comprehensive analysis of cells at the single-cell level are demanded. However, using traditional biological tools, such as petri-dishes and well-plates, is technically challengeable for manipulating and analyzing single-cells with small size and low concentration of target biomolecules. With the development of microfluidics, which is a technology of manipulating and controlling fluids in the range of micro- to pico-liters in networks of channels with dimensions from tens to hundreds of microns, single-cell study has been blooming for almost two decades. Comparing to conventional petri-dish or well-plate experiments, microfluidic single-cell analysis offers advantages of higher throughput, smaller sample volume, automatic sample processing, and lower contamination risk, etc., which made microfluidics an ideal technology for conducting statically meaningful single-cell research. In this review, we will summarize the advances of microfluidics for single-cell manipulation and analysis from the aspects of methods and applications. First, various methods, such as hydrodynamic and electrical approaches, for microfluidic single-cell manipulation will be summarized. Second, single-cell analysis ranging from cellular to genetic level by using microfluidic technology is summarized. Last, we will also discuss the advantages and disadvantages of various microfluidic methods for single-cell manipulation, and then outlook the trend of microfluidic single-cell analysis.

scholarly journals Quantitative PCR Analysis of DNA, RNAs, and Proteins in the Same Single Cell

2012 ◽  
Vol 58 (12) ◽  
pp. 1682-1691 ◽  
Author(s):  
Anders Ståhlberg ◽  
Christer Thomsen ◽  
David Ruff ◽  
Pierre Åman
Keyword(s):  
Single Cell ◽  
Quantitative Pcr ◽  
Single Cell Analysis ◽  
Basic Unit ◽  
Proximity Ligation Assay ◽  
Single Cell Level ◽  
Cell Analysis ◽  
Cell Level ◽  
Correlation Studies ◽  
Intracellular Concentrations

BACKGROUND The single cell represents the basic unit of all organisms. Most investigations have been performed on large cell populations, but understanding cell dynamics and heterogeneity requires single-cell analysis. Current methods for single-cell analysis generally can detect only one class of analytes. METHODS Reverse transcription and the proximity ligation assay were coupled with quantitative PCR and used to quantify any combination of DNA, mRNAs, microRNAs (miRNAs), noncoding RNAs (ncRNAs), and proteins from the same single cell. The method was used on transiently transfected human cells to determine the intracellular concentrations of plasmids, their transcribed mRNAs, translated proteins, and downstream RNA targets. RESULTS We developed a whole-cell lysis buffer to release unfractionated DNA, RNA, and proteins that would not degrade any detectable analyte or inhibit the assay. The dynamic range, analytical sensitivity, and specificity for quantifying DNA, mRNAs, miRNAs, ncRNAs, and proteins were shown to be accurate down to the single-cell level. Correlation studies revealed that the intracellular concentrations of plasmids and their transcribed mRNAs were correlated only moderately with translated protein concentrations (Spearman correlation coefficient, 0.37 and 0.31, respectively; P < 0.01). In addition, an ectopically expressed gene affected the correlations between analytes and this gene, which is related to gene regulation. CONCLUSIONS This method is compatible with most cell-sampling approaches, and generates output for the same parameter for all measured analytes, a feature facilitating comparative data analysis. This approach should open up new avenues in molecular diagnostics for detailed correlation studies of multiple and different classes of analytes at the single-cell level.

scholarly journals Single Cell Analysis Facilitates Staging of Blimp1-Dependent Primordial Germ Cells Derived from Mouse Embryonic Stem Cells

PLoS ONE ◽  
2011 ◽  
Vol 6 (12) ◽  
pp. e28960 ◽  
Author(s):  
John J. Vincent ◽  
Ziwei Li ◽  
Serena A. Lee ◽  
Xian Liu ◽  
Marisabel O. Etter ◽  
...  
Keyword(s):  
Stem Cells ◽  
Embryonic Stem Cells ◽  
Single Cell ◽  
Germ Cells ◽  
Single Cell Analysis ◽  
Primordial Germ Cells ◽  
Embryonic Stem ◽  
Mouse Embryonic Stem Cells ◽  
Cell Analysis

scholarly journals Dynamics of lineage commitment revealed by single-cell transcriptomics of differentiating embryonic stem cells

2016 ◽  
Author(s):  
Stefan Semrau ◽  
Johanna Goldmann ◽  
Magali Soumillon ◽  
Tarjei S. Mikkelsen ◽  
Rudolf Jaenisch ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stem Cells ◽  
Embryonic Stem Cells ◽  
Single Cell ◽  
Embryonic Stem ◽  
Lineage Commitment ◽  
Single Cell Level ◽  
Cell Level ◽  
Expression Variability ◽  
Gene Expression Heterogeneity

ABSTRACTGene expression heterogeneity in the pluripotent state of mouse embryonic stem cells (mESCs) has been increasingly well-characterized. In contrast, exit from pluripotency and lineage commitment have not been studied systematically at the single-cell level. Here we measured the gene expression dynamics of retinoic acid driven mESC differentiation using an unbiased single-cell transcriptomics approach. We found that the exit from pluripotency marks the start of a lineage bifurcation as well as a transient phase of susceptibility to lineage specifying signals. Our study revealed several transcriptional signatures of this phase, including a sharp increase of gene expression variability. Importantly, we observed a handover between two classes of transcription factors. The early-expressed class has potential roles in lineage biasing, the late-expressed class in lineage commitment. In summary, we provide a comprehensive analysis of lineage commitment at the single cell level, a potential stepping stone to improved lineage control through timing of differentiation cues.

A microsystem integrating photodegradable hydrogel microstructures and reconfigurable microfluidics for single-cell analysis and retrieval

Lab on a Chip ◽  
2015 ◽  
Vol 15 (3) ◽  
pp. 637-641 ◽  
Author(s):  
Kyung Jin Son ◽  
Dong-Sik Shin ◽  
Timothy Kwa ◽  
Jungmok You ◽  
Yandong Gao ◽  
...  
Keyword(s):  
Single Cell ◽  
Single Cell Analysis ◽  
Single Cell Level ◽  
Cell Analysis ◽  
Cell Secretion ◽  
Cell Level

We developed a micropatterned photodegradable hydrogel array integrated with reconfigurable microfluidics to enable cell secretion analysis and cell retrieval at the single-cell level.

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