Experimental and Computational Approaches for Single-Cell Enhancer Perturbation Assay

2019 ◽  
pp. 203-221 ◽  
Author(s):  
Shiqi Xie ◽  
Gary C. Hon
Keyword(s):  
Single Cell ◽  
Computational Approaches

scholarly journals Computational approaches for high‐throughput single‐cell data analysis

FEBS Journal ◽  
2018 ◽  
Vol 286 (8) ◽  
pp. 1451-1467 ◽  
Author(s):  
Helena Todorov ◽  
Yvan Saeys
Keyword(s):  
Data Analysis ◽  
Single Cell ◽  
High Throughput ◽  
Computational Approaches ◽  
Cell Data

EpiSort: Enumeration of cell types using targeted bisulfite sequencing

2019 ◽  
Author(s):  
Dvir Aran ◽  
Ron S. Dover ◽  
Karen E. Lundy ◽  
Michael D. Leipold ◽  
Ji Xuhuai ◽  
...  
Keyword(s):  
Tumor Microenvironment ◽  
Single Cell ◽  
Bisulfite Sequencing ◽  
Cell Types ◽  
Cellular Composition ◽  
Computational Approaches ◽  
Targeted Bisulfite Sequencing ◽  
Therapy Efficacy ◽  
Novel Strategy ◽  
Cancer Studies

AbstractThe cellular composition of tumors is now recognized as an essential phenotype, with implications to diagnostic, progression and therapy efficacy. A tool for accurate profiling of the tumor microenvironment is lacking, as single-cell methods and computational approaches are not applicable or suffer from low accuracy. Here we present EpiSort, a novel strategy based on targeted bisulfite sequencing, which allows the accurate enumeration of 23 cell types and may be applicable to cancer studies.

scholarly journals Measuring and Modelling the Epithelial- Mesenchymal Hybrid State in Cancer: Clinical Implications

2021 ◽  
pp. 1-24
Author(s):  
Mohit Kumar Jolly ◽  
Ryan J. Murphy ◽  
Sugandha Bhatia ◽  
Holly J. Whitfield ◽  
Andrew Redfern ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Cancer Progression ◽  
Validation Studies ◽  
Therapeutic Potential ◽  
Prognostic Significance ◽  
Clinical Implications ◽  
Computational Approaches ◽  
Hybrid State ◽  
Important Mediator

The epithelial-mesenchymal (E/M) hybrid state has emerged as an important mediator of elements of cancer progression, facilitated by epithelial mesenchymal plasticity (EMP). We review here evidence for the presence, prognostic significance, and therapeutic potential of the E/M hybrid state in carcinoma. We further assess modelling predictions and validation studies to demonstrate stabilised E/M hybrid states along the spectrum of EMP, as well as computational approaches for characterising and quantifying EMP phenotypes, with particular attention to the emerging realm of single-cell approaches through RNA sequencing and protein-based techniques.

Computational approaches for inferring tumor evolution from single-cell genomic data

2018 ◽  
Vol 7 ◽  
pp. 16-25 ◽  
Author(s):  
Hamim Zafar ◽  
Nicholas Navin ◽  
Luay Nakhleh ◽  
Ken Chen
Keyword(s):  
Single Cell ◽  
Genomic Data ◽  
Tumor Evolution ◽  
Computational Approaches

scholarly journals Leveraging Novel Integrated Single-Cell Analyses to Define HIV-1 Latency Reversal

Viruses ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1197
Author(s):  
Suhui Zhao ◽  
Athe Tsibris
Keyword(s):  
Data Analysis ◽  
Antiretroviral Therapy ◽  
Single Cell ◽  
Recent Work ◽  
High Throughput ◽  
Computational Approaches ◽  
Integrative Data Analysis ◽  
Viral Genomes ◽  
Infection Models ◽  
Hiv 1

While suppressive antiretroviral therapy can effectively limit HIV-1 replication and evolution, it leaves behind a residual pool of integrated viral genomes that persist in a state of reversible nonproductive infection, referred to as the HIV-1 reservoir. HIV-1 infection models were established to investigate HIV-1 latency and its reversal; recent work began to probe the dynamics of HIV-1 latency reversal at single-cell resolution. Signals that establish HIV-1 latency and govern its reactivation are complex and may not be completely resolved at the cellular and regulatory levels by the aggregated measurements of bulk cellular-sequencing methods. High-throughput single-cell technologies that characterize and quantify changes to the epigenome, transcriptome, and proteome continue to rapidly evolve. Combinations of single-cell techniques, in conjunction with novel computational approaches to analyze these data, were developed and provide an opportunity to improve the resolution of the heterogeneity that may exist in HIV-1 reactivation. In this review, we summarize the published single-cell HIV-1 transcriptomic work and explore how cutting-edge advances in single-cell techniques and integrative data-analysis tools may be leveraged to define the mechanisms that control the reversal of HIV-1 latency.

scholarly journals ChromVAR: Inferring transcription factor variation from single-cell epigenomic data

2017 ◽  
Author(s):  
Alicia N. Schep ◽  
Beijing Wu ◽  
Jason D. Buenrostro ◽  
William J. Greenleaf
Keyword(s):  
Transcription Factor ◽  
Single Cell ◽  
De Novo ◽  
Single Cells ◽  
R Package ◽  
Chromatin Accessibility ◽  
Data Sets ◽  
Sequence Motifs ◽  
Computational Approaches

AbstractSingle cell ATAC-seq (scATAC) yields sparse data that makes application of conventional computational approaches for data analysis challenging or impossible. We developed chromVAR, an R package for analyzing sparse chromatin accessibility data by estimating the gain or loss of accessibility within sets of peaks sharing the same motif or annotation while controlling for known technical biases. chromVAR enables accurate clustering of scATAC-seq profiles and enables characterization of known, or the de novo identification of novel, sequence motifs associated with variation in chromatin accessibility across single cells or other sparse epigenomic data sets.

scholarly journals Measuring and Modelling the Epithelial Mesenchymal Hybrid State in Cancer: Clinical Implications

2020 ◽  
Author(s):  
Mohit Kumar Jolly ◽  
Ryan J. Murphy ◽  
Sugandha Bhatia ◽  
Holly J. Whitfield ◽  
Melissa J. Davis ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Cancer Progression ◽  
Clinical Implications ◽  
Computational Approaches ◽  
Hybrid State ◽  
Important Mediator

The epithelial-mesenchymal (E/M) hybrid state has emerged as an important mediator of the elements of cancer progression facilitated by epithelial mesenchymal plasticity (EMP). We review here the evidence for the presence and prognostic potential of E/M hybrid state in carcinoma, modelling predictions and validations studies to demonstrate stabilised E/M hybrid intermediates along the spectrum of EMP, and computational approaches for characterising and quantifying EMP phenotypes, with particular attention to the emerging realm of single-cell approaches through RNA sequencing and protein-based approaches.

scholarly journals COTAN: Co-expression Table Analysis for scRNA-seq data

2020 ◽  
Author(s):  
S. G. Galfrè ◽  
F. Morandin ◽  
M. Pietrosanto ◽  
F. Cremisi ◽  
M. Helmer-Citterich
Keyword(s):  
Single Cell ◽  
State Transition ◽  
Computational Method ◽  
Single Cell Level ◽  
Cell Level ◽  
Computational Approaches ◽  
Table Analysis ◽  
A Cell ◽  
Low Efficiency ◽  
Cell Gene

AbstractEstimating co-expression of cell identity factors in single-cell transcriptomes is crucial to decode new mechanisms of cell state transition. Due to the intrinsic low efficiency of single-cell mRNA profiling, novel computational approaches are required to accurately infer gene co-expression in a cell population. We introduce COTAN, a statistical and computational method to analyze the co-expression of gene pairs at single cell level, providing the foundation for single-cell gene interactome analysis.

Electron microscopy of keratinocytes cultured on a collagen substrate used as an allograft for the treatment of chronic wounds

1992 ◽  
Vol 50 (2) ◽  
pp. 1104-1105
Author(s):  
Debby A. Jennings ◽  
Michael J. Morykwas ◽  
Louis C. Argenta
Keyword(s):  
Electron Microscopy ◽  
Cell Suspension ◽  
Single Cell ◽  
Chronic Wounds ◽  
Mechanical Stability ◽  
Uv Light ◽  
Type I ◽  
Single Cell Suspension ◽  
Collagen Substrate ◽  
Dermal Collagen

Grafts of cultured allogenic or autogenic keratlnocytes have proven to be an effective treatment of chronic wounds and burns. This study utilized a collagen substrate for keratinocyte and fibroblast attachment. The substrate provided mechanical stability and augmented graft manipulation onto the wound bed. Graft integrity was confirmed by light and transmission electron microscopy.Bovine Type I dermal collagen sheets (100 μm thick) were crosslinked with 254 nm UV light (13.5 Joules/cm2) to improve mechanical properties and reduce degradation. A single cell suspension of third passage neonatal foreskin fibroblasts were plated onto the collagen. Five days later, a single cell suspension of first passage neonatal foreskin keratinocytes were plated on the opposite side of the collagen. The grafts were cultured for one month.The grafts were fixed in phosphate buffered 4% formaldehyde/1% glutaraldehyde for 24 hours. Graft pieces were then washed in 0.13 M phosphate buffer, post-fixed in 1% osmium tetroxide, dehydrated, and embedded in Polybed 812.

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