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Results Found: 35
  • 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
  • Breast Invasive Carcinoma (TCGA, PanCancer Atlas) data

    Description

    This dataset contains summary data visualizations and clinical data from a broad sampling of 1,084 breast invasive carcinomas from 1,084 patients. The data was gathered as part of the PanCancer Atlas initiative, which aims to answer big, overarching questions about cancer by examining the full set of tumors characterized in the robust TCGA dataset. The clinical data includes mutation count, information...

    Subject
    Breast Neoplasms
    Carcinoma, Ductal, Breast
    Carcinoma, Lobular
    DNA Mutational Analysis
    Access Rights
    Free to All
  • MSK-IMPACT Clinical Sequencing Cohort (MSKCC, Nat Med 2017): Targeted sequencing of 10,000 clinical cases using the MSK-IMPACT assay

    Description

    This dataset contains summary data visualizations and clinical data from the targeted sequencing of 10,000 clinical cases using the MSK-IMPACT assay. The clinical data includes mutation count, information about mutated genes, tumor mutational burden calculations, tissue site from which the sample was derived, tumor purity among other relevant data points. The data set also includes copy-number segment...

    Subject
    Adenocarcinoma
    Adenocarcinoma of Lung
    Adenocarcinoma, Mucinous
    Breast Neoplasms
    Carcinoma, Ductal, Breast
    Carcinoma, Hepatocellular
    Carcinoma, Lobular
    Carcinoma, Non-Small-Cell Lung
    Carcinoma, Renal Cell
    Carcinoma, Squamous Cell
    Carcinosarcoma
    Cholangiocarcinoma
    Colonic Neoplasms
    Colorectal Neoplasms
    Cystadenocarcinoma, Serous
    DNA Mutational Analysis
    Gallbladder Neoplasms
    Glioblastoma
    Liposarcoma
    Lung Neoplasms
    Lymphoma, Follicular
    Melanoma
    Mesothelioma
    Neoplasms, Squamous Cell
    Neurofibroma
    Oligodendroglioma
    Osteosarcoma
    Ovarian Neoplasms
    Pancreatic Neoplasms
    Prostatic Neoplasms
    Rectal Neoplasms
    Sarcoma
    Sarcoma, Synovial
    Squamous Cell Carcinoma of Head and Neck
    Stomach Neoplasms
    Thyroid Cancer, Papillary
    Urinary Bladder Neoplasms
    Uterine Neoplasms
    Uveal Neoplasms
    Access Rights
    Free to All
  • 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
  • SUMMIT - Neratinib Basket Study (Multi-Institute, Nature 2018): MSK-IMPACT sequencing of 86 patients with HER2- and HER3-mutant cancers

    Description

    This dataset contains summary data visualizations and clinical data from a broad sampling of HER2- and HER3-mutant tumors. The data was generated utilizing the MSK-IMPACT targeted sequencing test. The clinical data includes tumor type (based on the opensource OncoTree ontology developed at MSK), mutation count, information about mutated genes, Amplification Status, Best objective response rate, Bubble...

    Subject
    Breast Neoplasms
    Carcinoma, Hepatocellular
    Carcinoma, Non-Small-Cell Lung
    Carcinoma, Renal Cell
    Colorectal Neoplasms
    DNA Mutational Analysis
    Endometrial Neoplasms
    Esophageal Neoplasms
    Genes, erbB
    Genes, erbB-2
    Melanoma
    Ovarian Neoplasms
    Pancreatic Neoplasms
    Salivary Gland Neoplasms
    Sarcoma
    Skin Neoplasms
    Urinary Bladder Neoplasms
    Uterine Cervical Neoplasms
    Access Rights
    Free to All
  • NCI-60 Cell Lines (NCI, Cancer Res 2012): Whole-exome sequencing of 67 samples by NCI-60 cell line project

    Description

    This dataset contains summary data visualizations and clinical data from 67 samples from 67 patients as part an NCI-60 cell line project to compile NCI-60 cell line high-throughput and high-content data into CellMiner, a genomic and pharmacologic database created by the National Cancer Center Institute. The clinical data includes deidentified patient and sample IDs, mutation counts, detailed cancer...

    Subject
    Adenocarcinoma
    Brain Neoplasms
    Breast Neoplasms
    Carcinoma, Renal Cell
    Colorectal Neoplasms
    DNA Mutational Analysis
    Leukemia, Myeloid
    Lung Neoplasms
    Melanoma
    Ovarian Neoplasms
    Prostatic Neoplasms
    Access Rights
    Free to All
  • Breast Invasive Carcinoma (TCGA, Firehose Legacy)

    Description

    TCGA Breast Invasive Carcinoma. Source data from GDAC Firehose. Previously known as TCGA Provisional. This dataset contains summary data visualizations and clinical data from a broad sampling of 1,108 carcinomas from 1,101 patients. The data was gathered as part of the Broad Institute of MIT and Harvard Firehose initiative, a cancer analysis pipeline. The clinical data includes mutation count, information...

    Subject
    Breast Neoplasms
    Carcinoma, Ductal, Breast
    Carcinoma, Lobular
    DNA Mutational Analysis
    Skin Neoplasms
    Access Rights
    Free to All