Genome-wide molecular recording using Live-seq

Chen, W; Guillaume‐Gentil, Orane; Dainese, Riccardo; Py, Rainer; Zachara, Magda; Cg, Gäbelein; Vorholt, Julia A.; Deplancke, Bart

doi:10.1101/2021.03.24.436752

Cited by 12 publications

(12 citation statements)

References 71 publications

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“…They concluded that baseline levels of the protein NFKBIA (IκBα) and cell cycle state as the major determinants of the observed phenotypic changes. 159 As with all the technologies mentioned here, scRNA-seq will undoubtedly continue to develop and become cheaper which will allow for more widespread use. With this will come more information which will be useful in deciphering the complex immune responses that occur in healthy and diseased cells.…”

Section: Direct Rna Sequencingmentioning

confidence: 99%

“…Live-seq is a new innovative approach designed to allow for sampling of single cells during a live immune response. 159 It can act as a recorder and allow researchers to evaluate the immune response in the same cell overtime. This technology was used to study macrophages sampled both at baseline and following LPS stimulation over time.…”

Section: Direct Rna Sequencingmentioning

confidence: 99%

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What sequencing technologies can teach us about innate immunity*

Salih

Carpenter

2021

Immunological Reviews

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For years, we have taken a reductionist approach to understanding gene regulation through the study of one gene in one cell at a time. While this approach has been fruitful it is laborious and fails to provide a global picture of what is occurring in complex situations involving tightly coordinated immune responses. The emergence of wholegenome techniques provides a system-level view of a response and can provide a plethora of information on events occurring in a cell from gene expression changes to splicing changes and chemical modifications. As with any technology, this often results in more questions than answers, but this wealth of knowledge is providing us with an unprecedented view of what occurs inside our cells during an immune response. In this review, we will discuss the current RNA-sequencing technologies and what they are helping us learn about the innate immune system.

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Section: Direct Rna Sequencingmentioning

confidence: 99%

Section: Direct Rna Sequencingmentioning

confidence: 99%

What sequencing technologies can teach us about innate immunity*

Salih

Carpenter

2021

Immunological Reviews

View full text Add to dashboard Cite

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“…It is worth noting that cells were viable up to five days post-extraction and that viability was dependent on the volume extracted from cytoplasm and nucleoplasm. In an extension of this work, Chen et al 111 developed a technique called Live-Seq. Standard single cell RNA sequencing involves lysis, thus providing a snapshot and endpoint measurement.…”

Section: Single Cell Samplingmentioning

confidence: 99%

Extending applications of AFM to fluidic AFM in single living cell and extracellular vesicle studies

Qiu

Chien

Maroulis

et al. 2021

Preprint

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In this article, a review of the application of atomic force microscopy (AFM) for the analyses of extracellular vesicles is presented. This information is then extended to include fluidic Atomic Force Microscopy (fluidic AFM) applications. Fluidic AFM is an offshoot of AFM that combines a microfluidic cantilever with AFM and has enabled the research community to conduct biological, pathological, and pharmacological studies on cells at the single-cell level in a liquid environment. AFM applications involving single cell and extracellular vesicle studies, colloidal force spectroscopy, and single cell adhesion measurements are discussed. In this review, new results are offered, using fluidic AFM, to illustrate (1) the speed with which sequential measurements of adhesion using coated colloid beads can be done, (2) the ability to assess lateral binding forces (LBFs) of endothelial or epithelial cells in a confluent cell monolayer in appropriate physiological environment, and (3) the ease of measurement of vertical binding force (VBFs) of intercellular adhesion between heterogeneous cells. Finally, key applications are discussed that include extracellular vesicle absorption, manipulation of a single living cell by intracellular injection, sampling of cellular fluid from a single living cell, patch clamping, and mass measurements of a single living cell.

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“…With the exception of proof-of-concept methods still too nascent to be widely applied (Chen et al, 2021), omics measurements of single-cells are generally destructive, preventing measurement of a cell at more than a single time point. As a result, most single-cell measurements for studying dynamic processes are of a "snapshot" nature, imposing inherent limitations on the study of such processes from this data (Weinreb et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

singlecellVR: Interactive Visualization of Single-Cell Data in Virtual Reality

et al. 2021

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Single-cell assays have transformed our ability to model heterogeneity within cell populations. As these assays have advanced in their ability to measure various aspects of molecular processes in cells, computational methods to analyze and meaningfully visualize such data have required matched innovation. Independently, Virtual Reality (VR) has recently emerged as a powerful technology to dynamically explore complex data and shows promise for adaptation to challenges in single-cell data visualization. However, adopting VR for single-cell data visualization has thus far been hindered by expensive prerequisite hardware or advanced data preprocessing skills. To address current shortcomings, we present singlecellVR, a user-friendly web application for visualizing single-cell data, designed for cheap and easily available virtual reality hardware (e.g., Google Cardboard, ∼$8). singlecellVR can visualize data from a variety of sequencing-based technologies including transcriptomic, epigenomic, and proteomic data as well as combinations thereof. Analysis modalities supported include approaches to clustering as well as trajectory inference and visualization of dynamical changes discovered through modelling RNA velocity. We provide a companion software package, scvr to streamline data conversion from the most widely-adopted single-cell analysis tools as well as a growing database of pre-analyzed datasets to which users can contribute.

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Genome-wide molecular recording using Live-seq

Cited by 12 publications

References 71 publications

What sequencing technologies can teach us about innate immunity*

What sequencing technologies can teach us about innate immunity*

Extending applications of AFM to fluidic AFM in single living cell and extracellular vesicle studies

singlecellVR: Interactive Visualization of Single-Cell Data in Virtual Reality

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