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111,247 results for “cells”
STING OPS: HeLa Genome-wide Screen Single-Cell Features (Part 1/5)
<div> <div> <p><strong>Classification and functional characterization of regulators of intracellular STING trafficking identified by genome-wide optical pooled screening</strong></p> <p>Single-cell features and coordinates for HeLa genome-wide screen, Zenodo dataset part 1/5.</p> <p>Images available at gs://opspublic-east1/STINGOpticalPooledScreen/Images/GW*.</p> <p>README for additional image information is at gs://opspublic-east1/STINGOpticalPooledScreen/STING_README.</p> </div> </div>
Exploring the potential of biphenylamine and triphenylamine-based sensitizers for enhanced efficiency more than 8% in dye-sensitized solar cells
<p>Due to the world's rapidly expanding population and industrial sector, which raises the demand for energy, solar cells can address both global energy and environmental needs. With the aim to enhance the dye-sensitized solar cell (DSSC) efficiency, we designed four metal-free BPA and TPA-based dyes (RK2-RK5) by increasing the donor strength (substituting different groups such as biphenylamine (BPA) and triphenylamine (TPA) in the donor side of the dye) based on the reference dye (RK1) as such dye showed improved DSSC's power conversion efficiency. Density functional theory (DFT) was applied at the B3LYP/6-31G** level to calculate the ground-state (S<sub>0</sub>) optimized geometries of (RK1-RK5). Time-dependent DFT (TD-DFT) was utilized to compute the absorption spectra utilizing four functionals (B3LYP, CAM-B3LYP, PBE1PBE and BHandHLYP) in gas phase and solvent such as dichloromethane (DCM) and ethanol. The comprehensive analysis of RK1-RK5 as well as dyes@TiO<sub>2</sub> was performed, and light was shed on the optoelectronic properties. Frontier molecular orbitals' (FMOs') charge density distribution revealed the sensitizers' intramolecular charge transfer (ICT) from the donor to the acceptor moiety. After adsorption charge transfer was noticed from sensitizer to the TiO<sub>2</sub> semiconductor's surface in dyes@TiO<sub>2</sub>. Dyes adsorption on the TiO<sub>2</sub> cluster would be stable, as revealed by the dyes@TiO<sub>2</sub> cluster's negative binding energy. Additionally, it was found that double donor raises the electronic coupling and electron injection constants in RK4 and RK5, indicating that the charge injection in these newly designed dyes would be superior. As a result, the DSSC efficiency in newly designed derivatives has been improved to 8.05% for RK5 by substituting TPA unit at R1 and R2 position in parent compound. These well-established correlations between structure-property relationship, and performance provide profound insight into how improving the donor moiety strength in organic sensitizers affects device performance. It boosted photovoltaic performance through enhanced short-circuit current density, and light-harvesting efficiency. For high-efficiency in DSSCs, it can be a useful rational molecular designing strategy for D-π -A organic sensitizers.</p>
STING OPS: HeLa Genome-wide Screen Single-Cell Features (Part 3/5)
<div> <div> <p><strong>Classification and functional characterization of regulators of intracellular STING trafficking identified by genome-wide optical pooled screening</strong></p> <p>Single-cell features and coordinates for HeLa genome-wide screen, Zenodo dataset part 3/5.</p> <p>Images available at gs://opspublic-east1/STINGOpticalPooledScreen/Images/GW*.</p> <p>README for additional image information is at gs://opspublic-east1/STINGOpticalPooledScreen/STING_README.</p> </div> </div>
STING OPS: HeLa Genome-wide Screen Single-Cell Features (Part 4/5)
<div> <div> <p><strong>Classification and functional characterization of regulators of intracellular STING trafficking identified by genome-wide optical pooled screening</strong></p> <p>Single-cell features and coordinates for HeLa genome-wide screen, Zenodo dataset part 4/5.</p> <p>Images available at gs://opspublic-east1/STINGOpticalPooledScreen/Images/GW*.</p> <p>README for additional image information is at gs://opspublic-east1/STINGOpticalPooledScreen/STING_README.</p> </div> </div>
The effect of extracellular vesicles derived from oral squamous cell carcinoma on the metabolic profile of oral fibroblasts
<p><span>Oral cancer is one of the most common forms of head and neck cancers. Oral squamous cell carcinoma (OSCC) accounts for more than 90% of the oral malignancies. The molecular pathogenesis of OSCC is complex as it involves altered expression of specific genes and proteins, but also comprises changes in metabolic processes. It is suggested that extracellular vesicles (EVs) released by cancer cells may contribute to cancer development and metastasis by recruiting and changing phenotype of normal cells that surround the tumor. The aim of the project was to characterize the effect of OSCC EVs on the metabolic profile of normal oral fibroblasts (NOFs). Targeted </span><span>liquid chromatography-mass spectrometry metabolic profiling was performed on control cells and NOFs exposed to OSCC EVs for 24 and 48 h. Analysis of detected metabolites revealed that OSCC EVs affected NOFs the most after 24 h of exposure. Among metabolites that were significantly altered at 24 h, </span><span>pyruvate, ATP, UTP, coenzyme A, and dihydroxyacetone phosphate were upregulated, while fatty acids such as nervonic acid, linoleate, oleate, palmitoleic acid, and docosahexaenoic acid were downregulated. These findings were supported by Western blotting of pyruvate kinase M2 (PKM2). The metabolic pathways of glycolysis, </span><span>citric acid cycle, and </span><span>amino acid metabolism were enriched, suggesting that OSCC EVs cause phenotype switch in NOFs that may contribute to </span><span>acquiring</span><span> a pro-tumorigenic phenotype.</span></p>
SN2N's 3D dataset of outer mitochondrial membrane network of live COS-7 cells labeled with Tom20-mCherry on SD-SIM sysytem.
Open the record for dataset details and reuse information.
Adaptative Survival of Aspergillus fumigatus to Echinocandins Arises from Cell Wall Remodeling Beyond β-1,3-glucan Synthesis Inhibition
<p>Unprocessed Solid-state NMR and Molecular Dynamics data sets for the manuscript titled "Adaptative Survival of Aspergillus fumigatus to Echinocandins Arises from Cell Wall Remodeling Beyond β-1,3-glucan Synthesis Inhibition"</p>
The TCR assigns naive T cells to a preferred lymph node
<p>Naive T cells recirculate between the spleen and lymph nodes where they mount immune responses when meeting dendritic cells presenting foreign antigen. As this may happen anywhere, naive T cells ought to visit all lymph nodes. Here, deep sequencing almost-complete TCR-repertoires led to a comparison of different lymph nodes within and between individual mice. We find strong evidence for a deterministic CD4/CD8 lineage choice and a consistent spatial structure. Specifically, some T cells show a preference for one or multiple lymph nodes, suggesting that their TCR interacts with locally presented (self-)peptides. These findings are mirrored in TCR-transgenic mice showing localized CD69-expression, retention, and cell division. Thus, naïve T cells intermittently sense antigenically dissimilar niches, which is expected to affect their homeostatic competition.</p>
Raw Data for "Synthesis and functionalisation of biodegradable Second Harmonic Generation nanoprobes for cell targeting"
<p>Raw data files used in the "Synthesis and functionalisation of biodegradable Second Harmonic Generation nanoprobes for cell targeting" manuscript.</p>
Figure 3 in Cytotoxicity of extracts and compounds isolated from Croton echioides in animal tumor cell (HTC)
Figure 3. Clerodan diterpenes tested.
Data from: Aged-vascular niche hinders osteogenesis of mesenchymal stem cells through paracrine repression of Wnt-axis
<p>Raw data set for: Fleischhacker V, Milosic F, Bricelj M, Kührer K, Wahl-Figlash K, Heimel P, Diendorfer A, Nardini E, Fischer I, Stangl H, Pietschmann P, Hackl M, Foisner R, Grillari J, Hengstschläger M, and Osmanagic-Myers S. Aged-vascular niche hinders osteogenesis of mesenchymal stem cells through paracrine repression of Wnt-axis. Aging Cell. 2024 Jun;23(6):e14139. doi: 10.1111/acel.14139. Epub 2024 Apr 5.</p> <p><span>Age-induced decline in osteogenic potential of bone marrow mesenchymal stem cells (BMSCs) potentiates osteoporosis and increases risk for bone fractures. Despite e</span><span>pidemiology studies reporting concurrent development of vascular- and bone diseases in the elderly, the underlying mechanisms for the vascular-bone cross-talk in aging are largely unknown. </span><span>In this study, we show that accelerated endothelial aging deteriorates bone tissue through paracrine repression of Wnt-driven-axis in BMSCs. <span>Here, we utilize </span>physiologically aged mice<span> in conjunction with our transgenic endothelial progeria mouse model </span>(Hutchinson-Gilford progeria syndrome; HGPS) that<span> displays hallmarks of an aged bone marrow vascular niche</span>. We find bone defects associated with diminished BMSC osteogenic differentiation that implicate the existence of angiocrine factors with long-term inhibitory effects. microRNA-transcriptomics of HGPS-patient plasma combined with aged-vascular niche analyses in progeria mice reveal abundant secretion of Wnt-repressive microRNA-31-5p. Moreover, we show that inhibition of microRNA-31-5p as well as selective Wnt-activator CHIR99021 boost the osteogenic potential of BMSCs through de-repression and activation of the Wnt-signalling, respectively. Our results demonstrate that the vascular niche significantly contributes to osteogenesis defects in aging and pave ground for microRNA-based therapies of bone loss in elderly.</span></p> <h1> </h1>
Increased spatial coupling of integrin and collagen IV in the immunoresistant clear-cell renal-cell carcinoma tumor microenvironment - Nanostring CosMx SMI Data
<p>Data export from Nanostring CosMx SMI, directly from Nanostring, in Seurat Object format for use in R. Clear cell renal cell carcinoma and papillary renal cell carcinoma were profiled before and after exposure to immunotherapy, with and without sarcomatoid features in clear cell tumors. Each tumor had a field of view in the stromal compartment and field of view in the tumor compartment.</p> <p>For appropriate clinical information associated with this study, please contact Dr. Brandon Manley.</p>
Data for Isotype-aware Inference of B cell Clonal Lineage Trees from Single-cell Sequencing Data
<p>This is the accompanying data to the manuscript titled<em> Isotype-aware Inference of B cell Clonal Lineage Trees from Single-cell Sequencing Data</em>. To reproduce the TRIBAL output please use this <a href="https://doi.org/10.5281/zenodo.12741290">code repository</a> as the arguments and codebase may have changed since release. </p>
CD4+ T cells re-wire granuloma cellularity and regulatory networks, promoting immunomodulation following Mtb reinfection
<p>Here we include the necessary .ipynb, .h5ad, and .rds (used for cell-cell interaction analyses) files used in our work: "Immunomodulatory re-wiring of granuloma cellularity and regulatory networks by CD4 T cells following Mtb reinfection"</p>
AI classification of normal and malignant cells on the basis of their viscoelastic properties
Open the record for dataset details and reuse information.
Diversity of group 1 innate lymphoid cells in human tissues
<p>Group 1 innate lymphoid cells (ILC1s) are cytotoxic and interferon gamma-producing lymphocytes lacking antigen-specific receptors, which include ILC1s and natural killer (NK) cells. In mice, ILC1s differ from NK cells, as they develop independently of the NK-specifying transcription factor EOMES, while requiring the repressor ZFP683 (ZNF683 in humans) for tissue residency. Here we identify highly variable ILC1 subtypes across tissues through investigation of human ILC1 diversity by single-cell RNA sequencing and flow cytometry. The intestinal epithelium contained abundant mature EOMES<sup>-</sup> ILC1s expressing PRDM1 rather than ZNF683, alongside a few immature TCF7<sup>+</sup>PRDM1<sup>-</sup> ILC1s. Other tissues harbored NK cells expressing ZNF683 and EOMES transcripts; however, EOMES protein content was variable. These ZNF683<sup>+</sup> NK cells are tissue-imprinted NK cells phenotypically resembling ILC1s. The tissue ILC1-NK spectrum also encompassed conventional NK cells and NK cells distinguished by PTGDS expression. These findings establish a foundation for evaluating phenotypic and functional changes within the NK-ILC1 spectrum in diseases.</p>
Single-cell analyses of polyclonal Plasmodium vivax infections and their consequences on parasite transmission Source Data
<p>Source Data for the paper by Hazzard et al. entitled <em>Single-cell analyses of polyclonal Plasmodium vivax infections and their consequences on parasite transmission</em>.</p>
Third FAIRmat users meeting Nov2023 - FAIR Data Principles in Perovskite Solar Cell Research using NOMAD - Daniel Baumann
<p>Daniel Baumann (doctoral research project at KIT in the group of Ulrich Paetzold) highlights how NOMAD Oasis supports experimental materials researchers in the field of perovskite photovoltaics. A live demonstration of experimental planning, documentation, as well as automated data evaluation is presented. Particularly, in conjunction with a highly repeatable robotic spin-coating setup, the realization of this vast potential may be closer than anticipated. </p>
BAM files of wild-type CP-A cells and the TP53 KO CP-A clones.
<p>BAM files (alignment to hg38) of wild-type CP-A cells and the TP53 knock-out (KO) CP-A clones (2c8, 3d2, 5f4). Please refer to Figure 2. of <span>doi:</span> https://doi.org/10.1101/2024.01.24.576991.</p>
HER2/neu-specific T-cells
<p>Single-cell RNA-seq data of HER2/neu-specific T-cells genereated with the BD Rhapsody™ system.</p> <p>Donor information: 3 healthy subjects, 2 male (SampleTag04, SampleTag05), 1 female (SampleTag06).</p> <p>Cell preparation: HER2/neu-specific T-cells were obtained via a Tetramer-based sorting of the naturally-occuring anti-CD3 and anti-CD28-activated T-cells co-cultured with the Dendritic cells that were maturated by a KIFGSLAFL peptide. </p> <p>Single-cell analysis system: BD Rhapsody™</p> <p>Library strategy: 5' mRNA sequencing</p> <p>Library preparation protocol: BD Rhapsody™ TCR/BCR Full Length, Targeted mRNA, and Sample Tag Library Preparation</p> <p>mRNA panel: BD Rhapsody™ Immune Response Panel HS</p> <p>BD Pipeline version: 1.11.1L</p>
ScienceDex guides
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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.