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Results Found: 39
  • Single-cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment - 5' RNA sequencing and TCR sequencing

    Authors
    Azizi, Elham
    Carr, Ambrose James
    Plitas, George
    Cornish, Andrew Erickson
    15 more author(s)...
    Description

    Single-cell RNA sequencing was performed on three patients using the 10x genomics TCR profiling kits. For each patient, populations of T-cells were assayed for both TCR sequence and trancriptome-wide RNA-sequence. Two donors have a replicate experiment. From the GEO summary: "Knowledge of immune cell phenotypes in the tumor microenvironment is essential for understanding mechanisms of cancer progression...

    Subject
    Breast Neoplasms
    Gene Expression Profiling
    Gene Expression Regulation, Neoplastic
    Immunotherapy
    Lymphocytes, Tumor-Infiltrating
    Receptors, Antigen, T-Cell
    Transcriptome
    Tumor Microenvironment/immunology
    Access Rights
    Free to All
  • Single-cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment 3' RNA Sequencing

    Authors
    Azizi, Elham
    Carr, Ambrose James
    Plitas, George
    Cornish, Andrew Erickson
    15 more author(s)...
    Description

    Single-cell RNA sequencing was performed on eight donors using the InDrop v2 protocol. For each donor populations of CD45+ immune cells were assayed for trancriptome-wide RNA-sequence. At least one replicate was taken for each donor. From the GEO summary: "Knowledge of immune cell phenotypes in the tumor microenvironment is essential for understanding mechanisms of cancer progression and immunotherapy...

    Subject
    Breast Neoplasms
    Gene Expression Profiling
    Gene Expression Regulation, Neoplastic
    Immunotherapy
    Lymphocytes, Tumor-Infiltrating
    Receptors, Antigen, T-Cell
    Transcriptome
    Tumor Microenvironment/immunology
    Access Rights
    Free to All
  • Flow Cytometry Datasets Associated with Single-cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment research

    Authors
    Cornish, Andrew Erickson
    Description

    The purpose of the dataset from the Flow Repository: "To determine the degree to which populations of intratumoral T cells, especially but not limited to T regs, initially found in single cell RNA sequencing data may be reproduced in mass cytometry data." From the description on Flow Repository: The data included for each of the 3 patients (BC12, BC13, and BC14, respectively) is presented in nine...

    Subject
    Breast Neoplasms
    Gene Expression Profiling
    Gene Expression Regulation, Neoplastic
    Immunotherapy
    Leukocytes, Mononuclear
    Lymphocytes, Tumor-Infiltrating
    Tumor Microenvironment/immunology
    Timeframe
    2018
    Access Rights
    Free to All
  • R Codebase for BISCUIT: Infinite Mixture Model to cluster and impute single cells

    Authors
    Prabhakaran, Sandhya
    Azizi, Elham
    Carr, Ambrose James
    Pe'er, Dana
    Description

    BISCUIT (Bayesian Inference for Single-cell ClUstering and ImpuTing) provides a method for the iterative normalization and cluster of single-cell gene RNA-seq expression data. BISCUIT eases clustering of cells based on similar gene expression after correcting technical variation. The software uses a Bayesian model and employs a model driven by covariance structures for the normalization and the input...

    Subject
    Bayes Theorem
    Gene Expression Profiling
    Transcriptome
    Access Rights
    Free to All
  • A Molecular Taxonomy of Urothelial Carcinoma

    Authors
    Sjödahl, Gottfrid
    Lauss, Martin
    Lindgren, David
    Höglund, Mattias
    Description

    Summary from the GEO: " Even though urothelial cancer (UC) is the fourth common tumor type among males, progress in treatment development has been deficient. Pathological assessment provides the urologists with only a broad classification, complicated by frequent disagreement among pathologist and the co-existence of different grading systems. Consequently, there is a great need for an objective,...

    Subject
    Gene Expression Profiling
    Urinary Bladder Neoplasms
    Access Rights
    Free to All
  • Nodal signaling maintains H3K18ac landscape to promote mesendodermal differentiation through TRIM33

    Authors
    Luo, Maoguo
    Bai, Jianbo
    Liu, Bofeng
    Yan, Peiqiang
    13 more author(s)...
    Description

    ATAC-seq, RNA-seq, and ChIP-seq datasets supporting the article "H3K18ac Primes Mesendodermal Differentiation upon Nodal Signaling". From GEO authors' summary: "The epigenome of a cell is established and maintained by chromatin modifiers and remodelers, which are recruited to the chromatin by specific transcription factors. In this report, we show that nodal cross-talks with the epigenome through...

    Subject
    Gene Expression Profiling
    Transcription Factors
    Access Rights
    Free to All
  • RNA sequencing data for 30 bladder cancer cell lines

    Authors
    Lee, I-Ling
    McConkey, David J.
    Su, Xiaoping
    Choi, Woonyoung
    Description

    Summary from the GEO: "RNA-sequencing of a panel of urothelial cancer cells. The goal of the study is to examine the genome-wide expression profile in each of the 30 urothelial cancer cells tested in our laboratory." "Overall design: Each of the 30 cell lines was DNA fingerprinted to confirm its real identity. Total RNA was obtained from each cell line and subjected to Illumina RNA sequencing."...

    Subject
    Gene Expression Profiling
    Urinary Bladder Neoplasms
    Access Rights
    Free to All
  • Pan-Cancer Atlas (PanCanAtlas)

    Description

    The Pan-Cancer Atlas (PanCanAtlas) initiative aims to answer big, overarching questions about cancer by examining the full set of tumors characterized in the robust TCGA dataset. The Cancer Genome Atlas (TCGA) Research Network has profiled and analyzed large numbers of human tumors to discover molecular aberrations at the DNA, RNA, protein and epigenetic levels. The resulting rich data provide a major...

    Subject
    Gene Expression Profiling
    Neoplasms/genetics
    Oncogenes
    Signal Transduction
    Access Rights
    Free to All
    Free to all with registration
  • Organ-specific in situ transcriptomics of MDA231 cells identified by Flura-seq

    Alternate Title(s)
    Flura-seq identifies organ-specific adaptations in metastasis-initiating cells
    Authors
    Basnet, Harihar
    Tian, Lin
    Massagué, Joan
    Description

    Summary from the GEO: "Metastasis-initiating cells dynamically adapt to the distinct microenvironments of different organs, but these early adaptations are poorly understood due to the limited sensitivity of in situ transcriptomics. We developed fluorouracil-labeled RNA sequencing (Flura-seq) for in situ analysis with unprecedented sensitivity. Flura-seq utilizes cytosine deaminase (CD) to convert...

    Subject
    Brain Neoplasms
    Breast Neoplasms
    Gene Expression Profiling
    Lung Neoplasms
    Transcriptome
    Access Rights
    Free to All
  • Flura-Seq Identifies In Situ Transcriptomes of Micrometastases

    Authors
    Basnet, Harihar
    Macalinao, Danilo Reynaldo Galindez
    Massagué, Joan
    Description

    Summary from the GEO: "Understanding the biology of rare cell populations in the context of their microenvironment requires an accurate analysis of the transcriptomes of these cells as expressed in situ. We developed fluorouracil-tagged RNA sequencing (Flura-seq) to characterize the transcriptomes of small cell subpopulations from a whole organ in model systems. The method utilizes cytosine deaminase...

    Subject
    Brain Neoplasms
    Breast Neoplasms
    Gene Expression Profiling
    Lung Neoplasms
    Transcriptome
    Transforming Growth Factor beta
    Access Rights
    Free to All