The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform

Preyas Shah - One of the best experts on this subject based on the ideXlab platform.

  • massively parallel single cell chromatin landscapes of human immune cell development and intratumoral t cell exhaustion
    Nature Biotechnology, 2019
    Co-Authors: Ansuman T Satpathy, Jeffrey M Granja, Kathryn E Yost, Francesca Meschi, Geoffrey P Mcdermott, Brett N Olsen, Maxwell R Mumbach, Sarah E Pierce, Ryan M Corces, Preyas Shah
    Abstract:

    Understanding complex tissues requires single-cell Deconstruction of gene regulation with precision and scale. Here, we assess the performance of a massively parallel droplet-based method for mapping transposase-accessible chromatin in single cells using sequencing (scATAC-seq). We apply scATAC-seq to obtain chromatin profiles of more than 200,000 single cells in human blood and basal cell carcinoma. In blood, application of scATAC-seq enables marker-free identification of cell type-specific cis- and trans-regulatory elements, mapping of disease-associated enhancer activity and reconstruction of trajectories of cellular differentiation. In basal cell carcinoma, application of scATAC-seq reveals regulatory networks in malignant, stromal and immune cells in the tumor microenvironment. Analysis of scATAC-seq profiles from serial tumor biopsies before and after programmed cell death protein 1 blockade identifies chromatin regulators of therapy-responsive T cell subsets and reveals a shared regulatory program that governs intratumoral CD8+ T cell exhaustion and CD4+ T follicular helper cell development. We anticipate that scATAC-seq will enable the unbiased discovery of gene regulatory factors across diverse biological systems.

  • massively parallel single cell chromatin landscapes of human immune cell development and intratumoral t cell exhaustion
    bioRxiv, 2019
    Co-Authors: Ansuman T Satpathy, Jeffrey M Granja, Kathryn E Yost, Francesca Meschi, Geoffrey P Mcdermott, Brett N Olsen, Maxwell R Mumbach, Sarah E Pierce, Ryan M Corces, Preyas Shah
    Abstract:

    Abstract Understanding complex tissues requires single-cell Deconstruction of gene regulation with precision and scale. Here we present a massively parallel droplet-based platform for mapping transposase-accessible chromatin in tens of thousands of single cells per sample (scATAC-seq). We obtain and analyze chromatin profiles of over 200,000 single cells in two primary human systems. In blood, scATAC-seq allows marker-free identification of cell type-specific cis- and trans-regulatory elements, mapping of disease-associated enhancer activity, and reconstruction of trajectories of differentiation from progenitors to diverse and rare immune cell types. In basal cell carcinoma, scATAC-seq reveals regulatory landscapes of malignant, stromal, and immune cell types in the tumor microenvironment. Moreover, scATAC-seq of serial tumor biopsies before and after PD-1 blockade allows identification of chromatin regulators and differentiation trajectories of therapy-responsive intratumoral T cell subsets, revealing a shared regulatory program driving CD8+ T cell exhaustion and CD4+ T follicular helper cell development. We anticipate that droplet-based single-cell chromatin accessibility will provide a broadly applicable means of identifying regulatory factors and elements that underlie cell type and function.

Ansuman T Satpathy - One of the best experts on this subject based on the ideXlab platform.

  • massively parallel single cell chromatin landscapes of human immune cell development and intratumoral t cell exhaustion
    Nature Biotechnology, 2019
    Co-Authors: Ansuman T Satpathy, Jeffrey M Granja, Kathryn E Yost, Francesca Meschi, Geoffrey P Mcdermott, Brett N Olsen, Maxwell R Mumbach, Sarah E Pierce, Ryan M Corces, Preyas Shah
    Abstract:

    Understanding complex tissues requires single-cell Deconstruction of gene regulation with precision and scale. Here, we assess the performance of a massively parallel droplet-based method for mapping transposase-accessible chromatin in single cells using sequencing (scATAC-seq). We apply scATAC-seq to obtain chromatin profiles of more than 200,000 single cells in human blood and basal cell carcinoma. In blood, application of scATAC-seq enables marker-free identification of cell type-specific cis- and trans-regulatory elements, mapping of disease-associated enhancer activity and reconstruction of trajectories of cellular differentiation. In basal cell carcinoma, application of scATAC-seq reveals regulatory networks in malignant, stromal and immune cells in the tumor microenvironment. Analysis of scATAC-seq profiles from serial tumor biopsies before and after programmed cell death protein 1 blockade identifies chromatin regulators of therapy-responsive T cell subsets and reveals a shared regulatory program that governs intratumoral CD8+ T cell exhaustion and CD4+ T follicular helper cell development. We anticipate that scATAC-seq will enable the unbiased discovery of gene regulatory factors across diverse biological systems.

  • massively parallel single cell chromatin landscapes of human immune cell development and intratumoral t cell exhaustion
    bioRxiv, 2019
    Co-Authors: Ansuman T Satpathy, Jeffrey M Granja, Kathryn E Yost, Francesca Meschi, Geoffrey P Mcdermott, Brett N Olsen, Maxwell R Mumbach, Sarah E Pierce, Ryan M Corces, Preyas Shah
    Abstract:

    Abstract Understanding complex tissues requires single-cell Deconstruction of gene regulation with precision and scale. Here we present a massively parallel droplet-based platform for mapping transposase-accessible chromatin in tens of thousands of single cells per sample (scATAC-seq). We obtain and analyze chromatin profiles of over 200,000 single cells in two primary human systems. In blood, scATAC-seq allows marker-free identification of cell type-specific cis- and trans-regulatory elements, mapping of disease-associated enhancer activity, and reconstruction of trajectories of differentiation from progenitors to diverse and rare immune cell types. In basal cell carcinoma, scATAC-seq reveals regulatory landscapes of malignant, stromal, and immune cell types in the tumor microenvironment. Moreover, scATAC-seq of serial tumor biopsies before and after PD-1 blockade allows identification of chromatin regulators and differentiation trajectories of therapy-responsive intratumoral T cell subsets, revealing a shared regulatory program driving CD8+ T cell exhaustion and CD4+ T follicular helper cell development. We anticipate that droplet-based single-cell chromatin accessibility will provide a broadly applicable means of identifying regulatory factors and elements that underlie cell type and function.

Ryan M Corces - One of the best experts on this subject based on the ideXlab platform.

  • massively parallel single cell chromatin landscapes of human immune cell development and intratumoral t cell exhaustion
    Nature Biotechnology, 2019
    Co-Authors: Ansuman T Satpathy, Jeffrey M Granja, Kathryn E Yost, Francesca Meschi, Geoffrey P Mcdermott, Brett N Olsen, Maxwell R Mumbach, Sarah E Pierce, Ryan M Corces, Preyas Shah
    Abstract:

    Understanding complex tissues requires single-cell Deconstruction of gene regulation with precision and scale. Here, we assess the performance of a massively parallel droplet-based method for mapping transposase-accessible chromatin in single cells using sequencing (scATAC-seq). We apply scATAC-seq to obtain chromatin profiles of more than 200,000 single cells in human blood and basal cell carcinoma. In blood, application of scATAC-seq enables marker-free identification of cell type-specific cis- and trans-regulatory elements, mapping of disease-associated enhancer activity and reconstruction of trajectories of cellular differentiation. In basal cell carcinoma, application of scATAC-seq reveals regulatory networks in malignant, stromal and immune cells in the tumor microenvironment. Analysis of scATAC-seq profiles from serial tumor biopsies before and after programmed cell death protein 1 blockade identifies chromatin regulators of therapy-responsive T cell subsets and reveals a shared regulatory program that governs intratumoral CD8+ T cell exhaustion and CD4+ T follicular helper cell development. We anticipate that scATAC-seq will enable the unbiased discovery of gene regulatory factors across diverse biological systems.

  • massively parallel single cell chromatin landscapes of human immune cell development and intratumoral t cell exhaustion
    bioRxiv, 2019
    Co-Authors: Ansuman T Satpathy, Jeffrey M Granja, Kathryn E Yost, Francesca Meschi, Geoffrey P Mcdermott, Brett N Olsen, Maxwell R Mumbach, Sarah E Pierce, Ryan M Corces, Preyas Shah
    Abstract:

    Abstract Understanding complex tissues requires single-cell Deconstruction of gene regulation with precision and scale. Here we present a massively parallel droplet-based platform for mapping transposase-accessible chromatin in tens of thousands of single cells per sample (scATAC-seq). We obtain and analyze chromatin profiles of over 200,000 single cells in two primary human systems. In blood, scATAC-seq allows marker-free identification of cell type-specific cis- and trans-regulatory elements, mapping of disease-associated enhancer activity, and reconstruction of trajectories of differentiation from progenitors to diverse and rare immune cell types. In basal cell carcinoma, scATAC-seq reveals regulatory landscapes of malignant, stromal, and immune cell types in the tumor microenvironment. Moreover, scATAC-seq of serial tumor biopsies before and after PD-1 blockade allows identification of chromatin regulators and differentiation trajectories of therapy-responsive intratumoral T cell subsets, revealing a shared regulatory program driving CD8+ T cell exhaustion and CD4+ T follicular helper cell development. We anticipate that droplet-based single-cell chromatin accessibility will provide a broadly applicable means of identifying regulatory factors and elements that underlie cell type and function.

Sarah E Pierce - One of the best experts on this subject based on the ideXlab platform.

  • massively parallel single cell chromatin landscapes of human immune cell development and intratumoral t cell exhaustion
    Nature Biotechnology, 2019
    Co-Authors: Ansuman T Satpathy, Jeffrey M Granja, Kathryn E Yost, Francesca Meschi, Geoffrey P Mcdermott, Brett N Olsen, Maxwell R Mumbach, Sarah E Pierce, Ryan M Corces, Preyas Shah
    Abstract:

    Understanding complex tissues requires single-cell Deconstruction of gene regulation with precision and scale. Here, we assess the performance of a massively parallel droplet-based method for mapping transposase-accessible chromatin in single cells using sequencing (scATAC-seq). We apply scATAC-seq to obtain chromatin profiles of more than 200,000 single cells in human blood and basal cell carcinoma. In blood, application of scATAC-seq enables marker-free identification of cell type-specific cis- and trans-regulatory elements, mapping of disease-associated enhancer activity and reconstruction of trajectories of cellular differentiation. In basal cell carcinoma, application of scATAC-seq reveals regulatory networks in malignant, stromal and immune cells in the tumor microenvironment. Analysis of scATAC-seq profiles from serial tumor biopsies before and after programmed cell death protein 1 blockade identifies chromatin regulators of therapy-responsive T cell subsets and reveals a shared regulatory program that governs intratumoral CD8+ T cell exhaustion and CD4+ T follicular helper cell development. We anticipate that scATAC-seq will enable the unbiased discovery of gene regulatory factors across diverse biological systems.

  • massively parallel single cell chromatin landscapes of human immune cell development and intratumoral t cell exhaustion
    bioRxiv, 2019
    Co-Authors: Ansuman T Satpathy, Jeffrey M Granja, Kathryn E Yost, Francesca Meschi, Geoffrey P Mcdermott, Brett N Olsen, Maxwell R Mumbach, Sarah E Pierce, Ryan M Corces, Preyas Shah
    Abstract:

    Abstract Understanding complex tissues requires single-cell Deconstruction of gene regulation with precision and scale. Here we present a massively parallel droplet-based platform for mapping transposase-accessible chromatin in tens of thousands of single cells per sample (scATAC-seq). We obtain and analyze chromatin profiles of over 200,000 single cells in two primary human systems. In blood, scATAC-seq allows marker-free identification of cell type-specific cis- and trans-regulatory elements, mapping of disease-associated enhancer activity, and reconstruction of trajectories of differentiation from progenitors to diverse and rare immune cell types. In basal cell carcinoma, scATAC-seq reveals regulatory landscapes of malignant, stromal, and immune cell types in the tumor microenvironment. Moreover, scATAC-seq of serial tumor biopsies before and after PD-1 blockade allows identification of chromatin regulators and differentiation trajectories of therapy-responsive intratumoral T cell subsets, revealing a shared regulatory program driving CD8+ T cell exhaustion and CD4+ T follicular helper cell development. We anticipate that droplet-based single-cell chromatin accessibility will provide a broadly applicable means of identifying regulatory factors and elements that underlie cell type and function.

Maxwell R Mumbach - One of the best experts on this subject based on the ideXlab platform.

  • massively parallel single cell chromatin landscapes of human immune cell development and intratumoral t cell exhaustion
    Nature Biotechnology, 2019
    Co-Authors: Ansuman T Satpathy, Jeffrey M Granja, Kathryn E Yost, Francesca Meschi, Geoffrey P Mcdermott, Brett N Olsen, Maxwell R Mumbach, Sarah E Pierce, Ryan M Corces, Preyas Shah
    Abstract:

    Understanding complex tissues requires single-cell Deconstruction of gene regulation with precision and scale. Here, we assess the performance of a massively parallel droplet-based method for mapping transposase-accessible chromatin in single cells using sequencing (scATAC-seq). We apply scATAC-seq to obtain chromatin profiles of more than 200,000 single cells in human blood and basal cell carcinoma. In blood, application of scATAC-seq enables marker-free identification of cell type-specific cis- and trans-regulatory elements, mapping of disease-associated enhancer activity and reconstruction of trajectories of cellular differentiation. In basal cell carcinoma, application of scATAC-seq reveals regulatory networks in malignant, stromal and immune cells in the tumor microenvironment. Analysis of scATAC-seq profiles from serial tumor biopsies before and after programmed cell death protein 1 blockade identifies chromatin regulators of therapy-responsive T cell subsets and reveals a shared regulatory program that governs intratumoral CD8+ T cell exhaustion and CD4+ T follicular helper cell development. We anticipate that scATAC-seq will enable the unbiased discovery of gene regulatory factors across diverse biological systems.

  • massively parallel single cell chromatin landscapes of human immune cell development and intratumoral t cell exhaustion
    bioRxiv, 2019
    Co-Authors: Ansuman T Satpathy, Jeffrey M Granja, Kathryn E Yost, Francesca Meschi, Geoffrey P Mcdermott, Brett N Olsen, Maxwell R Mumbach, Sarah E Pierce, Ryan M Corces, Preyas Shah
    Abstract:

    Abstract Understanding complex tissues requires single-cell Deconstruction of gene regulation with precision and scale. Here we present a massively parallel droplet-based platform for mapping transposase-accessible chromatin in tens of thousands of single cells per sample (scATAC-seq). We obtain and analyze chromatin profiles of over 200,000 single cells in two primary human systems. In blood, scATAC-seq allows marker-free identification of cell type-specific cis- and trans-regulatory elements, mapping of disease-associated enhancer activity, and reconstruction of trajectories of differentiation from progenitors to diverse and rare immune cell types. In basal cell carcinoma, scATAC-seq reveals regulatory landscapes of malignant, stromal, and immune cell types in the tumor microenvironment. Moreover, scATAC-seq of serial tumor biopsies before and after PD-1 blockade allows identification of chromatin regulators and differentiation trajectories of therapy-responsive intratumoral T cell subsets, revealing a shared regulatory program driving CD8+ T cell exhaustion and CD4+ T follicular helper cell development. We anticipate that droplet-based single-cell chromatin accessibility will provide a broadly applicable means of identifying regulatory factors and elements that underlie cell type and function.