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Results Found: 29
  • Clinical Proteomic Tumor Analysis Consortium Data

    Alternate Title(s)
    CPTAC
    Description

    The Clinical Proteomic Tumor Analysis Consortium (CPTAC) analyzes cancer biospecimens by mass spectrometry, characterizing and quantifying their constituent proteins, or proteome. Proteomic analysis for each CPTAC study is carried out independently by Proteomic Characterization Centers (PCCs) using a variety of protein fractionation techniques, instrumentation, and workflows. Mass spectrometry and...

    Subject
    Chemical fractionation
    Genomics
    Mass spectrometry
    Proteome
    Access Rights
    Free to All
  • 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
  • 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
  • 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
  • Breast cancer single-cell whole genome sequencing: BioProject supporting "Novel insights into breast cancer copy number genetic heterogeneity revealed by single-cell genome sequencing"

    Description

    Single-cell genome sequencing of breast cancer. Raw sequence reads from 2,040 SRA experiments based on 18 BioSamples. This data was generated for the study "Novel insights into breast cancer copy number genetic heterogeneity revealed by single-cell genome sequencing." Published in eLife.

    Subject
    Breast Neoplasms
    Whole Genome Sequencing
    Access Rights
    Free to All
  • The Angiosarcoma Project - Count Me In (Nature Medicine, 2020)

    Description

    Dataset Summary Description: "The Angiosarcoma Project is an ongoing patient-driven initiative. This archived Angiosarcoma Project dataset was analyzed in the linked Nature Medicine 2020 manuscript, and is derived from 48 samples from 36 angiosarcoma patients. Angiosarcoma tumor specimens (FFPE) were subjected to whole-exome sequencing (along with matched germline whole-exome sequencing). In addition...

    Subject
    Adenocarcinoma
    Basal Cell Carcinoma
    Breast Neoplasms
    Hemangiosarcoma
    Hodgkin Disease
    Leukemia, Lymphocytic, Chronic, B-Cell
    Rectal Neoplasms
    Skin Neoplasms
    Thyroid Neoplasms
    Uterine Neoplasms
    Vulvar Neoplasms
    Access Rights
    Free to All
  • The Angiosarcoma Project (Provisional): an ongoing patient-driven initiative.

    Description

    Dataset Summary Description: "This provisional dataset is currently derived from 83 samples, including tumor specimens (FFPE and cfDNA) from 62 angiosarcoma patients subjected to WES (along with matched germline WES). This study includes genomic data, patient-reported data (pre-pended as PRD), medical record data (MedR), and pathology report data (PATH). As these data were generated in a research...

    Subject
    Basal Cell Carcinoma
    Breast Neoplasms
    Colorectal Neoplasms
    Hemangiosarcoma
    Hodgkin Disease
    Leukemia, Lymphocytic, Chronic, B-Cell
    Prostatic Neoplasms
    Rectal Neoplasms
    Skin Neoplasms
    Thyroid Neoplasms
    Uterine Neoplasms
    Vulvar Neoplasms
    Access Rights
    Free to All