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766 results for “phosphorylation”
Phosphorylated histone variant γH2Av is associated with chromatin insulators in Drosophila
<p>Chromatin insulators are responsible for orchestrating long-range interactions between enhancers and promoters throughout the genome and align with the boundaries of topologically associating domains (TADs). Here, we demonstrate an interaction between proteins that associate with the gypsy insulator and the phosphorylated histone variant H2Av (γH2Av), normally a marker of DNA double strand breaks. Gypsy insulator components colocalize with γH2Av throughout the genome, in polytene chromosomes and in diploid cells in which Chromatin IP data shows it is enriched at TAD boundaries. Mutation of insulator components prevents stable H2Av phosphorylation in polytene chromatin and phosphatase inhibition strengthens the association between insulator components and γH2Av and rescues γH2Av localization in insulator mutants. We also show that γH2Av is a component of insulator bodies, and that phosphatase activity is required for insulator body dissolution after recovery from osmotic stress. Together, our results indicate a novel mechanism linking the H2A variant γH2Av to insulator function. </p>
Phosphorylation regulated conformational diversity and topological dynamics of an intrinsically disordered nuclear receptor
<p>Molecular dynamics simulations of AF1c region of human glucocorticoid receptor and its phosphovariants as described in the below paper: </p> <p><strong>Phosphorylation regulated conformational diversity and topological dynamics of an intrinsically disordered nuclear receptor</strong></p> <p>Vasily Akulov, Alba Jiménez Panizo, Eva Estébanez-Perpiñá, John van Noort, Alireza Mashaghi</p> <p> </p> <p>The data related to this project has been deposited in two repositories. This repository contains the first part of the data; the second part can be found at the DOI: 10.5281/zenodo.13822438</p>
Assessment of the expression level of selected genes and protein phosphorylation of the PI3K/Akt signaling pathway in patients with colorectal cancer
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Data related to "Lysosomal damage triggers a p38 MAPK-dependent phosphorylation cascade to promote lysophagy via the small heat shock protein HSP27."
<p>Data used to generate figures, as well as all uncropped blots. Article abstract: "Maintenance of lysosomal integrity is essential for cell viability. Upon injury, lysosomes may be targeted for degradation via a selective form of autophagy known as lysophagy. The engulfment of a damaged lysosome by an autophagosome is mediated by the recruitment of adaptor proteins, including SQSTM1/p62. p62 promotes lysophagy via the formation of phase separated condensates in a mechanism that is regulated by the heat shock protein HSP27. Here, we demonstrate a direct interaction between HSP27 and p62. We used structural modeling to predict the binding interface between HSP27 and p62 and identify several disease-associated mutations that map to this interface. We used proteomics to identify post-translational modifications of HSP27 that regulate HSP27 recruitment to stressed lysosomes, finding robust phosphorylation at several serine residues. Next, we characterized the upstream signaling mechanism leading to HSP27 phosphorylation, and found that p38 MAPK and its effector kinase MK2 are activated upon lysosomal damage by the kinase mTOR and the production of intracellular reactive oxygen species (ROS). Increased ROS activates p38 MAPK, which in turn allows MK2-dependent phosphorylation of HSP27. Depletion of HSP27 or the inhibition of HSP27 phosphorylation alters the dynamics of p62 condensates on stressed lysosomes, significantly inhibiting p62-dependent lysophagy. Thus, we define a novel lysosomal quality control mechanism in which lysosomal injury triggers a p38 MAPK/MK2 signaling cascade promoting p62-dependent lysophagy. Further, this signaling cascade is activated by many cellular stressors, including oxidative and heat stress, suggesting that other forms of selective autophagy may be regulated by p38 MAPK/MK2/HSP27." </p>
Phosphorylated mTOR targets in the E13.5 mouse brain
<p>Staining of p-S6 S240/244 and p-4EBP1/2 T37/46 in embryonic day 13.5 whole mouse brain, cleared using iDISCO+ </p>
BME Weights for Non-Phosphorylated and 5-Phosphorylated 4E-BP2 ensembles generated with FastFloppyTail Deposited on the PED
<p>Bayesian Maximum Entropy (BME) weights for NP- and 5P-4E-BP2 ensembles deposited on the Protein Ensemble Database (PED). 5p_100* correspond to weights for the N = 100 5-phosphorylated conformer ensemble, np_1000* correspond to weights for the N = 1000 non-phosphorylated conformer ensemble respectively.</p>
Oxidative Phosphorylation Inhibitor IACS-010759 in Treating Patients With Relapsed or Refractory Acute Myeloid Leukemia
ClinicalTrials.gov study NCT02882321. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Tyrosine phosphorylation tunes chemical and thermal sensitivity of TRPV2 ion channel
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Tandem-affinity purification of OOPS-1 and SPE-11 and identification of phosphorylation sites on OOPS-1 and SPE-11
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Data from: Sperm competitive advantage of a rare mitochondrial haplogroup linked to differential expression of mitochondrial oxidative phosphorylation genes
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Data from: Protein kinase FaSnRK2.6 phosphorylates transcription factor FabHLH3 to regulate anthocyanin homeostasis during strawberry fruit ripening
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Saccharomyces cerevisiae protein phosphorylation and translation accuracy
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Data for: A novel and ubiquitous miRNA-involved regulatory module ensures precise phosphorylation of RNA polymerase II and proper transcription
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Phosphorylated histone variant γH2Av is associated with chromatin insulators in Drosophila
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Data from: Phosphorylation, disorder, and phase separation govern the behavior of Frequency in the fungal circadian clock
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Data from: eIF4E S209 phosphorylation licenses myc- and stress-driven oncogenesis
<p>Mutational activation of Wnt/Myc and RAS signaling promotes colorectal cancer (CRC) development and deregulates translation. Phosphorylation of the cap binding protein eIF4E (Serine 209) is commonly elevated in cancer such as CRC yet dispensable for normal development. To better understand an oncogenic role of eIF4ES209, we generated eIF4E (S209A/+) heterozygous knockin (4EKI) HCT 116 human colorectal cancer (CRC) cells. 4EKI had little or no effect on total eIF4E levels, cap binding or global translation, while markedly reduced HCT 116 cell growth in spheroids and mice. 4EKI strongly inhibited Myc and ATF4 translation, the integrated Stress Response (ISR)-dependent glutamine metabolic signature, AKT activation and proliferation in vivo. p-eIF4E was found to be highly elevated in CRC precursor lesions in mouse and human. 4EKI inhibited polyposis in APC+/min mice by suppressing Myc protein and AKT activation. Furthermore, mutant KRAS cooperated with p-eIF4E and Myc to promote ISR-dependent glutamine addition in various CRC cell lines, which was characterized by increased cell death, transcriptomic heterogeneity and immune suppression upon deprivation. These findings demonstrate a critical role of eIF4ES209-dependent translation in Myc and stress-driven oncogenesis and as a potential therapeutic vulnerability.</p>
Data from: Oxidative phosphorylation gene transcription in whitefish species pairs reveals patterns of parallel and non-parallel physiological divergence
Across multiple lakes in North America, lake whitefish (Coregonus clupeaformis) have independently evolved "dwarf" and "normal" sympatric species pairs that exhibit pronounced phenotypic and genetic divergence. In particular, traits associated with metabolism have been shown to be highly differentiated between whitefish species. Here, we examine the transcription of genes associated with all five mitochondrial and nuclear genome-encoded oxidative phosphorylation (OXPHOS) complexes, the primary physiological mechanism responsible for the production of ATP, in whitefish species pairs from Cliff Lake and Webster Lake in Maine, USA. We observed OXPHOS gene transcription divergence between dwarf and normal whitefish in each of the two lakes, with the former exhibiting transcription upregulation for genes associated with each of the OXPHOS complexes. We also observed a significant influence of lake on transcription levels for some of the genes, indicating that inter-lake ecological or genetic differences are contributing to variation in OXPHOS gene transcription levels. Together, our results support the hypothesis that metabolic divergence is a critical adaptation involved in whitefish speciation, and implicate OXPHOS gene upregulation as a factor involved in meeting the enhanced energetic demands of dwarf whitefish. Further examination of the links between this critical physiological pathway and ecological and genetic variation will provide insight into the fine-scale evolutionary dynamics at work in nature.
Analysis of huntingtin phosphorylations by mass spectrometry (2016/08/05)
<p>Huntingtin structure-function open lab notebook.</p>
A molecular basis for the presentation of phosphorylated peptides by HLA-B antigens (ANNOTATED MS2 SPECTRA OF PHOSPHOPEPTIDES)
<p>Phosphopeptides identified from the immunopeptidome of the C1R-B*40 cell line. </p> <p>Phosphopeptides identified from the proteome of the C1R-B*40 cell line. </p> <p>Phosphopeptides identified from the immunopeptidome of the GR cell line. </p>
Structural Rearrangement of the Serotonin Transporter Intracellular Gate Induced by Thr276 Phosphorylation
<p>Molecular dynamics trajectories for <em>Structural Rearrangement of the Serotonin Transporter Intracellular Gate Induced by Thr276 Phosphorylation</em> by Matthew C. Chan, Erik Procko, Diwakar Shukla.</p> <p> </p> <p> </p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.