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  • An Open Library of Human Kinase Domain Constructs for Automated Bacterial Expression

    Authors
    Albanese, Steven Kyle
    Parton, Daniel Lawrence
    Isik, Mehtap
    Rodriguez-Laureano, Lucelenie
    7 more author(s)...
    Description

    Source code, assay data, full expression results for all ABL1 constructs, wild-type kinases, and ABL1 and SRC mutants, plasmid libraries, and other supporting material for the generation of a library of human kinase domain constructs for automated bacterial expression. From the publication abstract, "Kinases play a critical role in cellular signaling and are dysregulated in a number of diseases,...

    Subject
    Bacteria/metabolism
    Binding sites
    Escherichia coli/metabolism
    Phosphorylation
    Protein Structure, Secondary
    Protein-Tyrosine Kinases
    Proto-Oncogene Proteins c-abl
    src-Family Kinases
    Access Rights
    Free to All
    Fee Required
  • Discovery of a Drug Candidate for GLIS3-Associated Diabetes

    Authors
    Amin, Sadaf
    Cook, Brandoch
    Zhou, Ting
    Ghazizadeh, Zaniar
    13 more author(s)...
    Description

    Comparison of WT and GLIS3-/- cells at various stages of human pancreatic differentiation. From Gene Expression Omnibus authors' summary: "Through development and use of a minimal component protocol for derivation of late stage pancreatic progenitors and beta-like cells, we compared WT and GLIS3-/- pancreatic cells at different stages and discovered that GLIS3-/- cells show an ectopic activation...

    Subject
    Cell Differentiation/genetics
    Diabetes Mellitus
    Human Embryonic Stem Cells
    Hypoglycemic Agents
    Insulin-Secreting Cells
    Transcription Factors
    Access Rights
    Free to All
  • High frequency intestinal microbiota sampling in allogeneic bone marrow transplant patients

    Description

    NCBI BioProject collection containing SRA Experiment data and BioSamples resulting from "high frequency intestinal microbiota sampling in allogeneic bone marrow transplant patients, part of a larger systems biology project examining factors that influence antibiotic resistance, with a focus on the pathogens Vancomycin-Resistant Enterococcus and Klebsiella pneumoniae".

    Subject
    Drug Resistance, Microbial
    Gastrointestinal Tract
    Microbiota
    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
  • Rectal Cancer (MSK,Nature Medicine 2019): MSK-IMPACT targeted sequencing of matched rectal cancer tumor and tumoroid samples

    Authors
    Ganesh, Karuna
    Wu, Chao
    O'Rourke, Kevin Patrick
    Szeglin, Bryan Charles
    46 more author(s)...
    Description

    This dataset contains summary data visualizations and clinical data of rectal cancer tumoroids based on massively parallel sequencing using the custom, Food and Drug Administration (FDA)-cleared tumor-profiling panel MSK Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT). The clinical data includes mutation count, information about mutated genes, Gene Panel, Impact TMB Score,...

    Subject
    DNA Mutational Analysis
    Rectal Neoplasms
    Rectal Neoplasms/genetics
    Access Rights
    Free to All
  • Anaplastic Oligodendroglioma and Anaplastic Oligoastrocytoma (MSKCC, Neuro Oncol 2017): Genomic characterization using next generation sequencing (NGS) in 22 Anaplastic Oligodendroglioma and Anaplastic Oligoastrocytomas.

    Authors
    Thomas, Alissa A.
    Abrey, Lauren E.
    Terziev, Robert
    Raizer, Jeffrey J.
    24 more author(s)...
    Description

    This dataset contains summary data visualizations and sequencing data of 22 anaplastic oligodendroglioma (AO) and anaplastic oligoastrocytoma (AOA) tumors from 19 patients following a trial using induction temozolomide (TMZ) followed by myeloablative high-dose chemotherapy (HDC) with autologous stem-cell transplant (ASCT) as a potential strategy to defer radiotherapy. The clinical data includes mutation...

    Subject
    Brain Neoplasms
    Chemoradiotherapy
    DNA Mutational Analysis
    Oligodendroglioma
    Temozolomide
    Access Rights
    Free to All
  • Bladder Cancer (MSKCC, Nat Genet 2016): Whole exome and targeted sequencing of 34 plasmacytoid-variant (signet ring cell) tumors of the bladder

    Authors
    Al-Ahmadie, Hikmat
    Iyer, Gopakumar Vasudeva
    Lee, Byron Hing Lung
    Scott, Sasinya Neka
    25 more author(s)...
    Description

    Whole-exome and targeted sequencing of plasmacytoid bladder cancer, an aggressive histologic variant with a high risk of disease-specific mortality. This dataset contains summary data visualizations and sequencing data of 34 plasmacytoid-variant (signet ring cell) tumors of the bladder from 31 patients. Clinical data includes detailed cancer type, mutation count, information about mutated genes, patient...

    Subject
    DNA Mutational Analysis
    Plasmacytoma/genetics
    Urinary Bladder Neoplasms
    Access Rights
    Free to All
  • Bladder Cancer (TCGA, Cell 2017): Comprehensive analysis of muscle-invasive bladder cancers characterized by multiple TCGA analytical platforms.

    Authors
    Robertson, A. Gordon
    Kim, Jaegil
    Al-Ahmadie, Hikmat
    Bellmunt, Joaquim
    39 more author(s)...
    Description

    This dataset contains summary data visualizations and clinical data for a list of oncogenic and likely oncogenic alterations in 413 samples in tumors of the bladder from 412 patients, gathered as part of a comprehensive molecular characterization of muscle-invasive bladder cancer. Clinical data includes mutation count, information about mutated genes, patient demographics, and American Joint Committee...

    Subject
    DNA Mutational Analysis
    Urinary Bladder Neoplasms
    Access Rights
    Free to All