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  • (Metabolome analysis data): Mutant ASXL1 induces age-related expansion of phenotypic hematopoietic stem cells through activation of Akt/mTOR pathway

    Authors
    Kitamura, Toshio
    Description

    Description from MassIVE: Somatic mutations of ASXL1 are frequently detected in age-related clonal hematopoiesis (CH). However, how ASXL1 mutations drive CH remains elusive. Using knockin (KI) mice expressing a C-terminally truncated form of ASXL1-mutant (ASXL1-MT), we examined the influence of ASXL1-MT on physiological aging in hematopoietic stem cells (HSCs). HSCs expressing ASXL1-MT display competitive...

    Subject
    Clonal Hematopoiesis
    Hematopoietic Stem Cells
    Metabolome
    Myelodysplastic Syndromes
    Access Rights
    Free to All
  • 33 patients with Monoclonal Gammopathy of Undetermined Significance (MGUS)

    Description

    Dataset Description from EGA: " Monoclonal gammopathy of undetermined significance (MGUS) is a premalignant precursor of multiple myeloma (MM) with a 1% risk of progression per year. Although targeted analyses have shown the presence of specific genetic abnormalities such as IGH translocations, RB1 deletion, 1q gain, hyperdiploidy or RAS genes mutations, little is known about molecular mechanism of...

    Subject
    Monoclonal Gammopathy of Undetermined Significance
    Multiple Myeloma
    Oncogene Proteins, Fusion
    Access Rights
    Application Required
  • 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
  • A Study to Evaluate Denosumab in Young Patients With Primary Breast Cancer (D-Beyond)

    Description

    Description from the EGA: " This is a prospective, single arm phase IIa trial in which patients with early breast cancer will receive pre-operatively two doses of denosumab 120mg subcutaneously one week apart (maximum 12 days) followed by surgery. Tumor, normal breast tissue and blood samples will be collected at baseline and at surgery. Post-operative treatment will be at the discretion of the investigator.Primary...

    Subject
    Breast Neoplasms
    Denosumab
    Immunohistochemistry
    Ki-67 Antigen
    RANK Ligand
    Access Rights
    Application Required
  • A collection of Whole-genome sequencing files from the Cancer Genome Atlas program on Adenocarcinoma, filtered from the GDC Data Portal

    Description

    The GDC Data Portal is a robust data-driven platform that allows cancer researchers and bioinformaticians to search and download cancer data for analysis. This dataset is a filtered search result in the GDC Data Portal for TCGA Project, Adenocarcinoma, Whole Genome Sequencing Reads. It consists of 196 BAM files and 99 cases.

    Subject
    Adenocarcinoma of Lung
    Access Rights
    Application Required
  • A genomic classifier improves prediction of metastatic disease within 5 years after surgery in node-negative high-risk prostate cancer patients managed by radical prostatectomy without adjuvant therapy

    Authors
    Klein, Eric A.
    Yousefi, Kasra
    Haddad, Zaid
    Choeurng, Voleak
    6 more author(s)...
    Description

    Summary from the GEO: "To determine whether adding Decipher to standard risk stratification tools (CAPRA-S and Stephenson nomogram) improves accuracy in prediction of metastatic disease within 5 years after surgery in men with adverse pathologic features after RP. The study population consisted of 182 patients selected from 2,641 men who underwent RP at the Cleveland Clinic between 1987-2008 who...

    Subject
    Prostatectomy
    Prostatic Neoplasms
    Access Rights
    Free to All
  • A multivalent signal-transducing model for the DNMT1-mediated maintenance DNA methylation

    Authors
    Wang, Gang G.
    Grimm, Sara A.
    Description

    Summary from the GEO: "Heterochromatin-specific histone modifications frequently coexist with mammalian DNA methylation to orchestrate a repressive chromatin state. However, it remains elusive how these epigenetic modifications crosstalk. Here, we report that the first bromoadjacent homology (BAH1) domain and the replication foci targeting sequence (RFTS) of maintenance DNA methyltransferase DNMT1...

    Subject
    DNA (Cytosine-5-)-Methyltransferase 1
    DNA Methylation
    Heterochromatin
    Histone Code
    Histones
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    Free to All
  • AICDA-induced epigenetic plasticity accelerates germinal center-derived lymphomagenesis

    Authors
    Teater, Matt
    Elemento, Olivier
    Melnick, Ari M.
    Description

    Summary from the GEO: "Epigenetic heterogeneity is emerging as a significant phenotypic feature of tumors. In diffuse large B-cell lymphomas (DLBCLs), increased cytosine methylation heterogeneity is associated with poor clinical outcome, yet the biological mechanisms driving epigenetic heterogeneity remain unclear. Activation-induced cytidine deaminase (AICDA), an enzyme that deaminates and facilitates...

    Subject
    Cytidine Deaminase
    Germinal Center
    Lymphoma, Large B-Cell, Diffuse
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    Free to All
  • ATAC-seq on parental and acquired resistant cells (AqR)

    Authors
    Weirauch, Matthew T.
    Parameswaran, Sreeja
    Description

    Summary from GEO: "Parental and AqR cells were obtained. DNA was purified and submited for sequencing. Differential chromatin accessiblity was observed. AqR cells were derived from parental cells by adding inhibitor (CAY10566) every 3 days until cells became resistant (at about 3 weeks)." Overall design: from GEO: "1 parental cell in duplicate and 1 AqR cell in duplicate was submitted and analyzed."...

    Subject
    Brain Neoplasms
    Glioblastoma
    Stearoyl-CoA Desaturase
    Access Rights
    Free to All
  • Acral Melanoma (TGEN, Genome Res 2017): Whole exome sequencing and transcriptome analysis of 34 Acral Melanoma patients (33 with matched normals)

    Authors
    Liang, Winnie S.
    Hendricks, William
    Kiefer, Jeffrey
    Schmidt, Jessica
    22 more author(s)...
    Description

    This dataset contains summary data visualizations and clinical data from a comprehensive genomic and transcriptomic analysis of 38 acral lentiginous melanomas (ALM) from 34 patients. The study was conducted to analyze ALM, a rare sun-shielded melanoma subtype of cutaneous melanoma (CM) which is associated with worse survival than other CM in an effort to delineate non-UV oncogenic mechanisms. The...

    Subject
    Chromosome Aberrations
    DNA Mutational Analysis
    Melanoma/genetics
    Melanoma/pathology
    Transcriptome
    Access Rights
    Free to All