Multiplexed single-cell in situ RNA analysis by reiterative hybridization

The ability to quantify a large number of varied transcripts in single cells in their native spatial context is crucial to accelerate our understanding of health and disease. Bulk cell RNA analysis masks the heterogeneity in the cell population, while the conventional RNA imaging approaches suffer from low multiplexing capacity. Recent advances in multiplexed fluorescence in situ hybridization (FISH) methods enable comprehensive RNA profiling in individual cells in situ. These technologies will have wide applications in many biological and biomedical fields, including cell type classification, signaling network analysis, tissue architecture, disease diagnosis and patient stratification, etc. In this minireview, we will present the recent technological advances of multiplexed single-cell in situ RNA profiling assays, discuss their advantages and limitations, describe their biological applications, highlight the current challenges, and propose potential solutions.

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In-Situ Dual Beam (FIBSEM) Techniques for Probe Pad Deposition and Dielectric Integrity Inspection in 0.2 μm Technology DRAM Single Cells

ISTFA 1999: Conference Proceedings from the 25th International Symposium for Testing and Failure Analysis ◽

10.31399/asm.cp.istfa1999p0311 ◽

1999 ◽

Author(s):

Gunnar Zimmermann ◽

Richard Chapman

Keyword(s):

Electron Beam ◽

Single Cell ◽

Single Cells ◽

Ion Beam ◽

Gate Oxide ◽

Ion Milling ◽

Dual Beam ◽

Sem Imaging ◽

Innovative Techniques

Abstract Dual beam FIBSEM systems invite the use of innovative techniques to localize IC fails both electrically and physically. For electrical localization, we present a quick and reliable in-situ FIBSEM technique to deposit probe pads with very low parasitic leakage (Ipara < 4E-11A at 3V). The probe pads were Pt, deposited with ion beam assistance, on top of highly insulating SiOx, deposited with electron beam assistance. The buried plate (n-Band), p-well, wordline and bitline of a failing and a good 0.2 μm technology DRAM single cell were contacted. Both cells shared the same wordline for direct comparison of cell characteristics. Through this technique we electrically isolated the fail to a single cell by detecting leakage between the polysilicon wordline gate and the cell diffusion. For physical localization, we present a completely in-situ FIBSEM technique that combines ion milling, XeF2 staining and SEM imaging. With this technique, the electrically isolated fail was found to be a hole in the gate oxide at the bad cell.

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Label-Free and Quantitative Dry Mass Monitoring for Single Cells during In Situ Culture

Cells ◽

10.3390/cells10071635 ◽

2021 ◽

Vol 10 (7) ◽

pp. 1635

Author(s):

Ya Su ◽

Rongxin Fu ◽

Wenli Du ◽

Han Yang ◽

Li Ma ◽

...

Keyword(s):

Cell Growth ◽

Single Cell ◽

Hela Cells ◽

Quantitative Measurement ◽

Single Cells ◽

Dry Mass ◽

Quantitative Detection ◽

Label Free ◽

Mass Sensitivity

Quantitative measurement of single cells can provide in-depth information about cell morphology and metabolism. However, current live-cell imaging techniques have a lack of quantitative detection ability. Herein, we proposed a label-free and quantitative multichannel wide-field interferometric imaging (MWII) technique with femtogram dry mass sensitivity to monitor single-cell metabolism long-term in situ culture. We demonstrated that MWII could reveal the intrinsic status of cells despite fluctuating culture conditions with 3.48 nm optical path difference sensitivity, 0.97 fg dry mass sensitivity and 2.4% average maximum relative change (maximum change/average) in dry mass. Utilizing the MWII system, different intrinsic cell growth characteristics of dry mass between HeLa cells and Human Cervical Epithelial Cells (HCerEpiC) were studied. The dry mass of HeLa cells consistently increased before the M phase, whereas that of HCerEpiC increased and then decreased. The maximum growth rate of HeLa cells was 11.7% higher than that of HCerEpiC. Furthermore, HeLa cells were treated with Gemcitabine to reveal the relationship between single-cell heterogeneity and chemotherapeutic efficacy. The results show that cells with higher nuclear dry mass and nuclear density standard deviations were more likely to survive the chemotherapy. In conclusion, MWII was presented as a technique for single-cell dry mass quantitative measurement, which had significant potential applications for cell growth dynamics research, cell subtype analysis, cell health characterization, medication guidance and adjuvant drug development.

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Single-Cell in Situ RNA Analysis With Switchable Fluorescent Oligonucleotides

Frontiers in Cell and Developmental Biology ◽

10.3389/fcell.2018.00042 ◽

2018 ◽

Vol 6 ◽

Cited By ~ 5

Author(s):

Lu Xiao ◽

Jia Guo

Keyword(s):

Single Cell ◽

Rna Analysis

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Using Scuba for In Situ Determination of Chlorophyll Distributions in Corals by Underwater Near Infrared Fluorescence Imaging

Journal of Marine Science and Engineering ◽

10.3390/jmse8010053 ◽

2020 ◽

Vol 8 (1) ◽

pp. 53

Author(s):

Thomas Oh ◽

Jittiwat Sermsripong ◽

Barry W. Hicks

Keyword(s):

Fluorescence Imaging ◽

Large Scale ◽

Near Infrared ◽

Fluorescent Proteins ◽

Fluorescence Emission ◽

Florida Keys ◽

Nir Fluorescence ◽

Novel Method ◽

Near Infrared Fluorescence Imaging

Studies reporting quantitation and imaging of chlorophyll in corals using visible fluorescent emission in the red near 680 nm can suffer from competing emission from other red-emitting pigments. Here, we report a novel method of selectively imaging chlorophyll distributions in coral in situ using only the near infrared (NIR) fluorescence emission from chlorophyll. Commercially available equipment was assembled that allowed the sequential imaging of visible, visible-fluorescent, and NIR-fluorescent pigments on the same corals. The relative distributions of chlorophyll and fluorescent proteins (GFPs) were examined in numerous corals in the Caribbean Sea, the Egyptian Red Sea, the Indonesian Dampier Strait, and the Florida Keys. Below 2 m depth, solar induced NIR chlorophyll fluorescence can be imaged in daylight without external lighting, thus, it is much easier to do than visible fluorescence imaging done at night. The distributions of chlorophyll and GFPs are unique in every species examined, and while there are some tissues where both fluorophores are co-resident, often tissues are selectively enriched in only one of these fluorescent pigments. Although laboratory studies have clearly shown that GFPs can be photo-protective, their inability to prevent large scale bleaching events in situ may be due to their limited tissue distribution.

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AFM and Fluorescence Microscopy of Single Cells with Simultaneous Mechanical Stimulation via Electrically Stretchable Substrates

Materials ◽

10.3390/ma14154131 ◽

2021 ◽

Vol 14 (15) ◽

pp. 4131

Author(s):

Natalia Becerra ◽

Barbara Salis ◽

Mariateresa Tedesco ◽

Susana Moreno Flores ◽

Pasquale Vena ◽

...

Keyword(s):

Cell Culture ◽

Fluorescence Microscopy ◽

Single Cell ◽

Spatial Resolution ◽

Single Cells ◽

Optical Microscope ◽

Average Cell ◽

Atomic Force ◽

Cell Stretcher

We have developed a novel experimental set-up that simultaneously, (i) applies static and dynamic deformations to adherent cells in culture, (ii) allows the visualization of cells under fluorescence microscopy, and (iii) allows atomic force microscopy nanoindentation measurements of the mechanical properties of the cells. The cell stretcher device relies on a dielectric elastomer film that can be electro-actuated and acts as the cell culture substrate. The shape and position of the electrodes actuating the film can be controlled by design in order to obtain specific deformations across the cell culture chamber. By using optical markers we characterized the strain fields under different electrode configurations and applied potentials. The combined setup, which includes the cell stretcher device, an atomic force microscope, and an inverted optical microscope, can assess in situ and with sub-micron spatial resolution single cell topography and elasticity, as well as ion fluxes, during the application of static deformations. Proof of performance on fibroblasts shows a reproducible increase in the average cell elastic modulus as a response to applied uniaxial stretch of just 4%. Additionally, high resolution topography and elasticity maps on a single fibroblast can be acquired while the cell is deformed, providing evidence of long-term instrumental stability. This study provides a proof-of-concept of a novel platform that allows in situ and real time investigation of single cell mechano-transduction phenomena with sub-cellular spatial resolution.

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Self-reporting transposons enable simultaneous readout of gene expression and transcription factor binding in single cells

10.1101/538553 ◽

2019 ◽

Cited By ~ 3

Author(s):

Arnav Moudgil ◽

Michael N. Wilkinson ◽

Xuhua Chen ◽

June He ◽

Alex J. Cammack ◽

...

Keyword(s):

Gene Expression ◽

Transcription Factor ◽

Single Cell ◽

Binding Sites ◽

Expression Profiles ◽

Single Cells ◽

Gene Expression Profiles ◽

Cell Types ◽

Specific Cell

AbstractIn situ measurements of transcription factor (TF) binding are confounded by cellular heterogeneity and represent averaged profiles in complex tissues. Single cell RNA-seq (scRNA-seq) is capable of resolving different cell types based on gene expression profiles, but no technology exists to directly link specific cell types to the binding pattern of TFs in those cell types. Here, we present self-reporting transposons (SRTs) and their use in single cell calling cards (scCC), a novel assay for simultaneously capturing gene expression profiles and mapping TF binding sites in single cells. First, we show how the genomic locations of SRTs can be recovered from mRNA. Next, we demonstrate that SRTs deposited by the piggyBac transposase can be used to map the genome-wide localization of the TFs SP1, through a direct fusion of the two proteins, and BRD4, through its native affinity for piggyBac. We then present the scCC method, which maps SRTs from scRNA-seq libraries, thus enabling concomitant identification of cell types and TF binding sites in those same cells. As a proof-of-concept, we show recovery of cell type-specific BRD4 and SP1 binding sites from cultured cells. Finally, we map Brd4 binding sites in the mouse cortex at single cell resolution, thus establishing a new technique for studying TF biology in situ.

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Accurate sub-population detection and mapping across single cell experiments with PopCorn

10.1101/485979 ◽

2018 ◽

Author(s):

Yijie Wang ◽

Jan Hoinka ◽

Teresa M Przytycka

Keyword(s):

Comparative Analysis ◽

Single Cell ◽

Single Cells ◽

Novel Method ◽

Cell Data

The identification of sub-populations of cells present in a sample and the comparison of such sub-populations across samples are among the most frequently performed analyzes of single-cell data. Current tools for these kinds of data, however, fall short in their ability to adequately perform these tasks. We introduce a novel method, PopCorn (single cell sub-Populations Comparison), allowing for the identification of sub-populations of cells present within individual experiments while simultaneously performing sub-populations mapping across these experiments. PopCorn utilizes several novel algorithmic solutions enabling the execution of these tasks with unprecedented precision. As such, PopCorn provides a much-needed tool for comparative analysis of populations of single cells.

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Direct correlation between motile behavior and protein abundance in single cells

10.1101/067918 ◽

2016 ◽

Author(s):

Yann S Dufour ◽

Sébastien Gillet ◽

Nicholas W Frankel ◽

Douglas B Weibel ◽

Thierry Emonet

Keyword(s):

Protein Expression ◽

Single Cell ◽

Phenotypic Diversity ◽

Single Cells ◽

Selective Advantage ◽

Single Cell Protein ◽

Cell Protein ◽

Chemotaxis Proteins

AbstractUnderstanding how stochastic molecular fluctuations affect cell behavior requires the quantification of both behavior and protein numbers in the same cells. Here, we combine automated microscopy with in situ hydrogel polymerization to measure single-cell protein expression after tracking swimming behavior. We characterized the distribution of non-genetic phenotypic diversity in Escherichia coli motility, which affects single-cell exploration. By expressing fluorescently tagged chemotaxis proteins (CheR and CheB) at different levels, we quantitatively mapped motile phenotype (tumble bias) to protein numbers using thousands of single-cell measurements. Our results disagreed with established models until we incorporated the role of CheB in receptor deamidation and the slow fluctuations in receptor methylation. Beyond refining models, our central finding is that changes in numbers of CheR and CheB affect the population mean tumble bias and its variance independently. Therefore, it is possible to adjust the degree of phenotypic diversity of a population by adjusting the global level of expression of CheR and CheB while keeping their ratio constant, which, as shown in previous studies, confers functional robustness to the system. Since genetic control of protein expression is heritable, our results suggest that non-genetic diversity in motile behavior is selectable, supporting earlier hypotheses that such diversity confers a selective advantage.

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Spatial charting of single cell transcriptomes in tissues

10.1101/2021.11.24.469915 ◽

2021 ◽

Author(s):

Nicholas Navin ◽

Runmin Wei ◽

Siyuan He ◽

Shanshan Bai ◽

Emi Sei ◽

...

Keyword(s):

Single Cell ◽

Spatial Organization ◽

Spatial Information ◽

Ductal Carcinoma ◽

Single Cells ◽

Cell Types ◽

Spatial Structures ◽

Tissue Sections ◽

Normal Mouse Brain

Single cell RNA sequencing (scRNA-seq) methods can profile the transcriptomes of single cells but cannot preserve spatial information. Conversely, spatial transcriptomics (ST) assays can profile spatial regions in tissue sections, but do not have single cell genomic resolution. Here, we developed a computational approach called SChart, that combines these two datasets to achieve single cell spatial mapping of cell types, cell states and continuous phenotypes. We applied SChart to reconstruct cellular spatial structures in existing datasets from normal mouse brain and kidney tissues to validate our approach. We also performed scRNA-seq and ST experiments on two ductal carcinoma in situ (DCIS) tissues and applied SChart to identify subclones that were restricted to different ducts, and specific T cell states adjacent to the tumor areas. Our data shows that SChart can accurately map single cells in diverse tissue types to resolve their spatial organization into cellular neighborhoods and tissue structures.

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