Search Tips
of 3 Next >
Results Found: 28
  • 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
  • Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes via Nonequilibrium Candidate Monte Carlo

    Authors
    Gill, Samuel
    Lim, Nathan
    Grinaway, Patrick
    Rustenburg, Ariën
    4 more author(s)...
    Description

    Accurately predicting protein-ligand binding affinities and binding modes is a major goal in computational chemistry, but even the prediction of ligand binding modes in proteins poses major challenges. Here, we focus on solving the binding mode prediction problem for rigid fragments. That is, we focus on computing the dominant placement, conformation, and orientations of a relatively rigid, fragment-like...

    Subject
    Binding sites
    Access Rights
    Free to All
  • Cellular states, clonal dynamics, and evolution in Pearson syndrome revealed via single-cell multi-omics [Celline_scATAC]

    Authors
    Lareau, Caleb A.
    Ludwig, Leif S.
    Description

    Summary from GEO: "Large deletions in mitochondrial DNA (mtDNA) have been linked to a variety of clinical pathologies, including somatic emergence in congenital disorders such as Pearson Syndrome (MIM:557000), a mitochondrial disease characterized by sideroblastic anemia and exocrine pancreas dysfunction. Here, we develop a multi-omics approach to quantify mtDNA deletion heteroplasmy and cell state...

    Subject
    Anemia, Sideroblastic
    Binding sites
    Fibroblasts
    Genomics
    Heteroplasmy/genetics
    Myelodysplastic Syndromes
    Single-Cell Analysis
    Access Rights
    Free to All
  • Cellular states, clonal dynamics, and evolution in Pearson syndrome revealed via single-cell multi-omics [PBMC_scATAC]

    Authors
    Lareau, Caleb A.
    Ludwig, Leif S.
    Description

    Summary from GEO: "Large deletions in mitochondrial DNA (mtDNA) have been linked to a variety of clinical pathologies, including somatic emergence in congenital disorders such as Pearson Syndrome (MIM:557000), a mitochondrial disease characterized by sideroblastic anemia and exocrine pancreas dysfunction. Here, we develop a multi-omics approach to quantify mtDNA deletion heteroplasmy and cell state...

    Subject
    Anemia, Sideroblastic
    Binding sites
    Genomics
    Heteroplasmy/genetics
    Leukocytes, Mononuclear
    Myelodysplastic Syndromes
    Single-Cell Analysis
    Access Rights
    Free to All
  • A double negative post-transcriptional regulatory circuit mediates the virgin behavioral state

    Authors
    Garaulet, Daniel L.
    Moro, Albertomaria
    Lai, Eric C
    Description

    Summary from GEO: "The survival and reproductive success of animals depends on the ability to harmonize their external behaviors with their internal states. For example, females conduct numerous social programs that are distinctive to virgins compared to post-mated and/or pregnant individuals. In Drosophila, the fact that the post-mating switch is initiated by seminal factors implies the default...

    Subject
    Binding sites
    Mutation
    RNA-Seq
    Sexual Behavior, Animal
    Transcription Factors
    Access Rights
    Free to All
  • STAT4 promotes Bhlhe40 induction to drive protective IFN-g from natural killer cells during viral infection [STAT4 CUT&RUN]

    Authors
    Kim, Hyunu
    Sun, Joseph C.
    Description

    Summary from GEO: "NK cells represent a cellular component of the mammalian innate immune system, and mount rapid responses against viral infection, including the secretion of the potent anti-viral effector cytokine IFN-g. Following mouse cytomegalovirus (MCMV) infection, Bhlhe40 was the most highly induced transcription factor in NK cells among the basic helix-loop-helix family. Bhlhe40 upregulation...

    Subject
    Basic Helix-Loop-Helix Transcription Factors
    Binding sites
    Chromatin Immunoprecipitation Sequencing
    Interferon-gamma
    Interleukin-12
    Interleukin-18
    Killer Cells, Natural
    Mouse Cytomegalovirus
    STAT4 Transcription Factor
    Access Rights
    Free to All
  • STAT4 promotes Bhlhe40 induction to drive protective IFN-g from natural killer cells during viral infection [BHLHE40 CUT&RUN]

    Authors
    Kim, Hyunu
    Sun, Joseph C.
    Description

    Summary from GEO: "NK cells represent a cellular component of the mammalian innate immune system, and mount rapid responses against viral infection, including the secretion of the potent anti-viral effector cytokine IFN-g. Following mouse cytomegalovirus (MCMV) infection, Bhlhe40 was the most highly induced transcription factor in NK cells among the basic helix-loop-helix family. Bhlhe40 upregulation...

    Subject
    Basic Helix-Loop-Helix Transcription Factors
    Binding sites
    Chromatin Immunoprecipitation Sequencing
    Interferon-gamma
    Interleukin-12
    Interleukin-18
    Killer Cells, Natural
    Mouse Cytomegalovirus
    STAT4 Transcription Factor
    Access Rights
    Free to All
  • YTHDC1-Hyper tribe uncover YTHDC1 binding sites in human leukemia cells

    Authors
    Cheng, Yuanming
    Chu, Karen
    Kharas, Michael G.
    Description

    Summary from GEO: "The goal of this study is to identify YTHDC1 binding targets in MOLM13 cells(AML)." Overall design from GEO: "MOLM-13 cells overexpressing YTHDC1-ADAR fusion or empty vector for 48 hours were harvested for RNA-seq to look for A-G editing events."

    Subject
    Adenosine Deaminase
    Binding sites
    Leukemia, Myeloid, Acute
    Nuclear Proteins
    RNA-Binding Proteins
    RNA-Seq
    Access Rights
    Free to All
  • ChIP-Seq in DU-145 (ATCC HTB-81) Prostate Cancer Cells of FOSL1, TAZ, TEAD1, YAP

    Authors
    Chen, Yu
    Khurana, Ekta
    Wong, Chen Khuan
    Xu, Duo
    Description

    Summary from GEO: "Genome-wide mapping of FOSL1, YAP, TAZ and TEAD1 binding sites in DU145 cells." Overall design from GEO: "Genome occupancy profiling of FOSL1, YAP, TAZ, and TEAD1 was performed in DU145 cells."

    Subject
    Binding sites
    Chromatin Immunoprecipitation Sequencing
    Chromosome Mapping
    Prostatic Neoplasms
    Access Rights
    Free to All
  • ChIP-Seq in MSK-PCa3 Prostate Cancer Organoids of FOSL1, TAZ, TEAD1, YAP

    Authors
    Chen, Yu
    Khurana, Ekta
    Wong, Chen Khuan
    Xu, Duo
    Description

    Summary from GEO: "Genome-wide mapping of FOSL1, YAP, TAZ and TEAD1 binding sites in MSK-PCa3 cells." Overall design from GEO: "Genome occupancy profiling of FOSL1, YAP, TAZ, and TEAD1 was performed in MSK-PCA3 cells."

    Subject
    Binding sites
    Chromatin Immunoprecipitation Sequencing
    Chromosome Mapping
    Prostatic Neoplasms
    Access Rights
    Free to All