scholarly journals CASB: A concanavalin A-based sample barcoding strategy for single-cell sequencing

2020 ◽  
Author(s):  
Liang Fang ◽  
Guipeng Li ◽  
Qionghua Zhu ◽  
Huanhuan Cui ◽  
Yunfei Li ◽  
...  
Keyword(s):  
Single Cell ◽  
Concanavalin A ◽  
Cancer Cell Line ◽  
High Sensitivity ◽  
Cost Effective ◽  
Subtle Difference ◽  
Single Cell Sequencing ◽  
Minimal Sample ◽  
Ifn Γ ◽  
Multiple Drugs

AbstractSample multiplexing facilitates single cell sequencing by reducing costs, revealing subtle difference between similar samples, and identifying artifacts such as cell doublets. However, universal and cost-effective strategies are rather limited. Here, we reported a Concanavalin A-based Sample Barcoding strategy (CASB), which could be followed by both single-cell mRNA and ATAC (assay for transposase accessible chromatin) sequencing techniques. The method involves minimal sample processing, thereby preserving intact transcriptomic or epigenomic patterns. We demonstrated its high labeling efficiency, high accuracy in assigning cells/nuclei to samples regardless of cell type and genetic background, as well as high sensitivity in detecting doublets by two applications: 1) CASB followed by scRNA-seq to track the transcriptomic dynamics of a cancer cell line perturbed by multiple drugs, which revealed compound-specific heterogeneous response; 2) CASB together with both snATAC-seq and scRNA-seq to illustrate the IFN-γ-mediated dynamic changes on epigenome and transcriptome profile, which identified the transcription factor underlying heterogeneous IFN-γ response.

scholarly journals MQuad enables clonal substructure discovery using single cell mitochondrial variants

2021 ◽  
Author(s):  
Aaron Wing Cheung Kwok ◽  
Chen Qiao ◽  
Rongting Huang ◽  
Mai-Har Sham ◽  
Joshua W. K. Ho ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Single Cell ◽  
Single Cells ◽  
High Sensitivity ◽  
Copy Number Variations ◽  
Sequencing Data ◽  
Single Nucleotide ◽  
Single Cell Sequencing ◽  
Mtdna Variants ◽  
Python Package

AbstractMitochondrial mutations are increasingly recognised as informative endogenous genetic markers that can be used to reconstruct cellular clonal structure using single-cell RNA or DNA sequencing data. However, there is a lack of effective computational methods to identify informative mtDNA variants in noisy and sparse single-cell sequencing data. Here we present an open source computational tool MQuad that accurately calls clonally informative mtDNA variants in a population of single cells, and an analysis suite for complete clonality inference, based on single cell RNA or DNA sequencing data. Through a variety of simulated and experimental single cell sequencing data, we showed that MQuad can identify mitochondrial variants with both high sensitivity and specificity, outperforming existing methods by a large extent. Furthermore, we demonstrated its wide applicability in different single cell sequencing protocols, particularly in complementing single-nucleotide and copy-number variations to extract finer clonal resolution. MQuad is a Python package available via https://github.com/single-cell-genetics/MQuad.

scholarly journals MODL-09. FEASIBILITY OF ACUTE SLICE CULTURE-SINGLE CELL SEQUENCING DRUG SCREENING AS A TOOL TO SELECT THERAPY FOR CHILDREN WITH RELAPSED BRAIN TUMORS

2020 ◽  
Vol 22 (Supplement_3) ◽  
pp. iii412-iii413
Author(s):  
Bradley Gampel ◽  
Luca Szalontay ◽  
Wenting Zhao ◽  
James Garvin ◽  
Chankrit Sethi ◽  
...  
Keyword(s):  
Brain Tumors ◽  
Single Cell ◽  
Drug Screening ◽  
Patient Specific ◽  
Small Scale ◽  
Specific Drug ◽  
Rna Seq ◽  
Drug Responses ◽  
Single Cell Sequencing ◽  
Multiple Drugs

Abstract Children with relapsed brain tumors are less responsive to treatment. These children often receive therapies without having any robust predictive method of potential benefit. Acute slice culturing(ASC) is a methodology permitting freshly operated tumor to undergo a culturing process preserving the tumor’s micro-environment. With the current study, we investigated the feasibility of obtaining therapeutically meaningful data in a timely manner (3–5 days), performing direct drug testing and single cell sequencing using ASC. Previously, we have combined ex vivo slices of intact, patient-derived Glioblastoma tissue with single-cell RNA-seq for small-scale drug screening and assessment of patient and cell type-specific drug responses. We generated slices from preclinical mouse glioma models and surgical specimens from adult Glioblastoma patients, as well as from children with relapsed Ependymomas, Medulloblastomas, and Gliomas. We demonstrated that these acute slices preserved both the tumor heterogeneity and tumor microenvironment observed in single-cell RNA-seq of cells directly isolated from tumor tissue. Testing drug responses, we then treated tissue slices from the Glioblastoma mouse models and different patients with multiple drugs and combinations. This technique allowed us to identify drug-induced transcriptional responses in specific subpopulations of tumor cells, patient-specific drug sensitivities, and drug effects conserved in both mouse and human tumors. Preliminary data suggests that we can apply this procedure within 5–7 days and provide real-time drug screening/single cell sequencing ASC results to Recurrent/ Progressive pediatric Low-Grade Gliomas, High Grade Gliomas, Ependymomas and Medulloblastomas.

scholarly journals CASB: a concanavalin A‐based sample barcoding strategy for single‐cell sequencing

2021 ◽  
Vol 17 (4) ◽  
Author(s):  
Liang Fang ◽  
Guipeng Li ◽  
Zhiyuan Sun ◽  
Qionghua Zhu ◽  
Huanhuan Cui ◽  
...  
Keyword(s):  
Single Cell ◽  
Concanavalin A ◽  
Single Cell Sequencing

A cost-effective quasi single-cell assay for deciphering of clonal architecture of leukemic cells

2020 ◽  
Author(s):  
A Komkov ◽  
A Miroshnichenkova ◽  
A Smirnova ◽  
E Komech ◽  
E Atapina ◽  
...  
Keyword(s):  
Single Cell ◽  
Cost Effective ◽  
Leukemic Cells ◽  
Clonal Architecture ◽  
Cell Assay

scholarly journals Differentiating and quantifying exosome secretion from a single cell using quasi-bound states in the continuum

Nanophotonics ◽  
2020 ◽  
Vol 9 (5) ◽  
pp. 1081-1086 ◽  
Author(s):  
Abdoulaye Ndao ◽  
Liyi Hsu ◽  
Wei Cai ◽  
Jeongho Ha ◽  
Junhee Park ◽  
...  
Keyword(s):  
Single Cell ◽  
Optical Sensors ◽  
Figure Of Merit ◽  
Bound States ◽  
Single Cell Analysis ◽  
Optical Cavity ◽  
High Sensitivity ◽  
Cell Secretion ◽  
The Continuum ◽  
Refractive Index Detection

AbstractOne of the key challenges in biology is to understand how individual cells process information and respond to perturbations. However, most of the existing single-cell analysis methods can only provide a glimpse of cell properties at specific time points and are unable to provide cell secretion and protein analysis at single-cell resolution. To address the limits of existing methods and to accelerate discoveries from single-cell studies, we propose and experimentally demonstrate a new sensor based on bound states in the continuum to quantify exosome secretion from a single cell. Our optical sensors demonstrate high-sensitivity refractive index detection. Because of the strong overlap between the medium supporting the mode and the analytes, such an optical cavity has a figure of merit of 677 and sensitivity of 440 nm/RIU. Such results facilitate technological progress for highly conducive optical sensors for different biomedical applications.

scholarly journals Gold–Carbon Nanocomposites for Environmental Contaminant Sensing

Micromachines ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 719
Author(s):  
Shahrooz Rahmati ◽  
William Doherty ◽  
Arman Amani Babadi ◽  
Muhamad Syamim Akmal Che Mansor ◽  
Nurhidayatullaili Muhd Julkapli ◽  
...  
Keyword(s):  
Environmental Pollutants ◽  
High Sensitivity ◽  
Environmental Crisis ◽  
World Population ◽  
Chemical Contaminants ◽  
Carbon Nanocomposites ◽  
Minimal Sample ◽  
Wide Range ◽  
And Control ◽  
Analytical Tools

The environmental crisis, due to the rapid growth of the world population and globalisation, is a serious concern of this century. Nanoscience and nanotechnology play an important role in addressing a wide range of environmental issues with innovative and successful solutions. Identification and control of emerging chemical contaminants have received substantial interest in recent years. As a result, there is a need for reliable and rapid analytical tools capable of performing sample analysis with high sensitivity, broad selectivity, desired stability, and minimal sample handling for the detection, degradation, and removal of hazardous contaminants. In this review, various gold–carbon nanocomposites-based sensors/biosensors that have been developed thus far are explored. The electrochemical platforms, synthesis, diverse applications, and effective monitoring of environmental pollutants are investigated comparatively.

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