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254 results for “cell fusion”
Exploring Data Evaluation Strategies for Enhanced Identification of Host Cell Proteins in Drug Products of Therapeutic Antibodies and Fc-Fusion Proteins
<p>This data repository contains all previously unpublished raw data files for the manuscript “Exploring Data Evaluation Strategies for Enhanced Identification of Host Cell Proteins in Drug Products of Therapeutic Antibodies and Fc-Fusion Proteins” by Wolfgang Esser-Skala, Marius Segl, Therese Wohlschlager, Veronika Reisinger, Johann Holzmann, and Christian G. Huber. See <em>readme.md</em> for further information.</p>
Progenitor like cell type of an MLL-EDC4 fusion in acute myeloid leukemia
<p>Transcriptome analysis by single cell sequencing provides valuable information on intratumor heterogeneity and developmental stages of acute myeloid leukemia (AML) as well as interactions of tumor cells with the microenvironment. However, it has been hardly applied to the subgroup of cases with translocations of the mixed lineage leukemia (<i>MLL</i>) gene for which the enhancer of mRNA decapping 4 (<i>EDC4</i>) gene was recently identified as a novel fusion partner <i>(MLL-EDC4</i>). In our study published in Blood Advances (Schuster et al., 2023; https://doi.org/10.1182/bloodadvances.2022009096), we compared different <i>MLL</i> translocations by single cell RNA sequencing of cells derived from peripheral blood or bone marrow. The <i>MLL</i>-<i>EDC4</i> positive cells almost exclusively showed a transcriptional profile of hematopoietic progenitor cells while leukemic cells of <i>MLL-MLLT3</i> and <i>MLL-ELL</i> fusions exhibited a more differentiated phenotype. The <i>MLL</i>-<i>EDC4</i> progenitor state was characterized by the upregulation of key transcriptional regulators in AML (<i>RUNX1, SOX4, HOPX</i>), target genes of <i>MYC</i> and interferon signaling as well as other genes known to play a critical role in hematopoiesis or leukemic stem cell activation (<i>CDK6, FLT3, NPM1</i>). Here, the scRNA-seq dataset of our study is provided. It contains six scRNA-seq read count matrices of the AML samples with MLL fusions as described in the table scRNA-seq_samples.xlsx. Further details are given in the publication associated with this dataset. </p>
Influence of environmental conditions on the fusion of cationic liposomes with living mammalian cells
<p>Lipid-based nanoparticles, also called vesicles or liposomes, can be used as carriers for drugs or many types of biological macromolecules including DNA and proteins. Efficiency and speed of cargo delivery are especially high for carrier vesicles that fuse with the cellular plasma membrane. This occurs for lipid mixture containing equal amounts of the cationic lipid DOTAP and a neutral lipid with an additional few percent of an aromatic substance. The fusion ability of such particles depends on lipid composition with phosphoethanolamine (PE) lipids favoring fusion and phosphatidyl-choline (PC) lipids endocytosis. Here we examined the effects of temperature, ionic strength, osmolality, and pH on fusion efficiency of cationic liposomes with Chinese hamster ovary (CHO) cells. The phase state of liposomes was analyzed by small angle neutron scattering (SANS). Our results showed that PC containing lipid membranes were organized in the lamellar phase. Here, fusion efficiency depended on buffer conditions and remained vanishingly small at physiological conditions. In contrast, SANS indicated the coexistence of very small (~ 50 nm) objects with larger, most likely lamellar structures for PE containing lipid particles. The fusion of such particles to cell membranes occurred with very high efficiency at all buffer conditions. We hypothesize that the altered phase state resulted in a highly reduced energetic barrier against fusion.</p>
Benchmarking Illumina RNA-seq fusion transcript detection methods - cancer cell lines RNA-seq
<p>Cancer cell line RNA-seq data (reads or names of reads from CCLE data) used for benchmarking Illumina-based fusion detection methods as used in:</p> <p>Haas, B.J., Dobin, A., Li, B. <em>et al.</em> Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods. <em>Genome Biol</em> <strong>20</strong>, 213 (2019). https://doi.org/10.1186/s13059-019-1842-9</p> <p> </p> <p>For CCLE data, direct sharing of fastq files was not possible. CCLE data must be obtained from:</p> <p> https://portals.broadinstitute.org/ccle/home</p> <p>Instead, the identifiers for the reads leveraged as part of our study are made available, and these reads can be extracted from the CCLE fastq files directly once obtained from the primary source.</p> <p><br>For the non-CCLE data, the exact reads leveraged by our study are made directly available here in fastq format.</p>
Uncovering bacterial hosts of class 1 integrons in an urban coastal aquatic environment with a single-cell fusion-polymerase chain reaction technology
<p>Horizontal gene transfer (HGT) is a key driver of bacterial evolution via transmission of genetic materials across taxa. Class 1 integrons are genetic elements that correlate strongly with anthropogenic pollution and contribute to the spread of antimicrobial resistance (AMR) genes via HGT. Despite their significance to human health, there is a shortage of robust, culture-free surveillance technologies for identifying uncultivated environmental taxa that harbour class 1 integrons. We developed a modified version of epicPCR (emulsion, paired isolation and concatenation PCR) that links class 1 integrons amplified from single bacterial cells to taxonomic markers from the same cells in emulsified aqueous droplets. Using this single-cell genomic approach and Nanopore sequencing, we successfully assigned class 1 integron gene cassette arrays containing mostly AMR genes to their hosts in coastal water samples that were affected by pollution. Our work presents the first application of epicPCR for targeting variable, multi-gene loci of interest. We also identified the <em>Rhizobacter</em> genus as novel hosts of class 1 integrons. These findings establish epicPCR as a powerful tool for linking taxa to class 1 integrons in environmental bacterial communities and offer the potential to direct mitigation efforts towards hotspots of class 1 integron-mediated dissemination of AMR.</p>
Cellentra Viable Cell Bone Matrix (VCBM) Anterior Cervical Discectomy and Fusion Outcomes Study (VCBM/MaxAn)
ClinicalTrials.gov study NCT02182843. IPD Sharing: NO. Countries: 1. Publications: 14.
A Study of Selpercatinib (LY3527723) in Participants With Advanced or Metastatic RET Fusion-Positive Non-Small Cell Lung Cancer
ClinicalTrials.gov study NCT04194944. IPD Sharing: YES. Countries: 26. Publications: 4.
A Study Evaluating Platinum-Pemetrexed-Atezolizumab (+/-Bevacizumab) for Patients With Stage IIIB/IV Non-squamous Non-small Cell Lung Cancer With EGFR Mutations, ALK Rearrangement or ROS1 Fusion Progr
ClinicalTrials.gov study NCT04042558. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Uncovering bacterial hosts of class 1 integrons in an urban coastal aquatic environment with a single-cell fusion-polymerase chain reaction technology
Open the record for dataset details and reuse information.
Microtubule networks in zebrafish hair cells facilitate presynapse transport and fusion during development
Open the record for dataset details and reuse information.
Arabidopsis guard cell vacuoles imaged after the induction of vacuole fusion
<p>Wild type Arabidopsis thaliana plants from the Columbia-0 ecotype were grown in soil at 22C with a 16 h photoperiod. Leaves from 4-week old plants were cut in the morning and immediately processed to generate epidermal peels. Briefly, a small leaf fragment was applied abaxially to a coverslip coated with medical adhesive and all but the bottommost layers of abaxial cells containing the stomata were scrapped away with a razor. 1 mm thick silicone isolators (GraceBio #664170) were used to create wells around the adhesive for incubations. Epidermal peels were immediately incubated in stomata buffer (MES pH 6.1). To induce stomatal closure, peels were incubated in closing buffer (10 mM MES pH 6.1, 40 mM malate, 5 mM CaCl2, 10 µM BCECF, 50 mM ABA (Sigma Aldrich A1049) at 22C in the dark for two hours. To induce stomatal opening or vacuole fusion, ABA-treated peels were incubated in opening buffer (10 mM MES pH 6.1, 50 mM KCl) supplemented with 10 µM BCECF (Fisher Scientific B1170) and either 3 µM fusicoccin (Sigma F0537) or 33 µM wortmannin (Sigma W3144). Wortmannin-treated peels were kept in the dark, while fusicoccin-treated peels were exposed to the light for up to 1 h. All concentrated stocks were first dissolved in DMSO. Images of leaf epidermal peels were acquired after ABA incubation and after 20, 40 and 60 min of fusicoccin or wortmannin treatments. <br><br>Confocal laser scanning microscopy was carried out in a Zeiss LSM 980 confocal microscope. Images were taken with a 40× FCS water objective (1.1 N.A.). Acquisition of BCECF fluorescence was accomplished with 405 nm laser excitation and 495-550 nm emission filter set. Images were acquired with an Airyscan detector with a pinhole size of 2.5 airy units.</p>
Cell features for "Datasets for "Predicting microsatellite instabilitiy from histology images with a three-level hierarchical graph fusion model""
<p>This repository contains features and corresponding coordinates of cells extracted from 430 and 326 histologic images from patients with colorectal and gastric cancers from the TCGA cohort (original whole section SVS images are freely available at https://portal.gdc.cancer.gov/). All images in this library are from formalin-fixed paraffin-embedded (FFPE) diagnostic sections (“DX” on the GDC Data Portal). This blog explains this in detail: http://www.andrewjanowczyk.com/download-tcga-digital-pathology-images-ffpe/</p> <p><strong>Preprocessing.</strong></p> <p>All SVS slices were pre-processed as follows.</p> <p>According to “Deep learning can predict microsatellite instability directly from histology in gastrointestinal cancer” these histology images were categorized into “MSS” (microsatellite stable) or “MSIMUT” (microsatellite unstable or highly mutated) and corresponded to the article dividing the training and test sets.<br><br></p> <p>The features of all cells were extracted by Hovernet and Transnuseg at 40x objective magnification for extraction masking and further feature extraction</p>
Basal cell carcinoma diagnosis with fusion of deep learning and telangiectasia features
<p>Telangiectasia masks dataset created on a subset of the ISIC18, ISIC19 training datasets and the NIH study dataset R43 CA153927-01 and CA101639-02A2. All annotations are for Basal Cell Carcinoma lesions. This is an expanded dataset that was initially used in “<a href="https://onlinelibrary.wiley.com/doi/10.1111/srt.13150">A Deep Learning Approach to Detect Blood Vessels in Basal Cell Carcinoma</a>”.</p> <p>A sample lesion image and the corresponding mask is provided for preview. Lesion images and masks have been uploaded as separate zipped folders that can be downloaded.</p>
Cabozantinib in Patients With RET Fusion-Positive Advanced Non-Small Cell Lung Cancer and Those With Other Genotypes: ROS1 or NTRK Fusions or Increased MET or AXL Activity
ClinicalTrials.gov study NCT01639508. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Safety Study of Mesenchymal Stem Cells and Spinal Fusion
ClinicalTrials.gov study NCT01552707. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Dendritic Cell (DC)/Myeloma Fusions in Combination With Nivolumab in Patients With Relapsed Multiple Myeloma
ClinicalTrials.gov study NCT03782064. IPD Sharing: YES. Countries: 1. Publications: 0.
Data from: Direct transfer of learned behaviour via cell fusion in non-neural organisms
Cell fusion is a fundamental phenomenon observed in all eukaryotes. Cells can exchange resources such as molecules or organelles during fusion. In this paper, we ask whether a cell can also transfer an adaptive response to a fusion partner. We addressed this question in the unicellular slime mould Physarum polycephalum, in which cell–cell fusion is extremely common. Slime moulds are capable of habituation, a simple form of learning, when repeatedly exposed to an innocuous repellent, despite lacking neurons and comprising only a single cell. In this paper, we present a set of experiments demonstrating that slime moulds habituated to a repellent can transfer this adaptive response by cell fusion to individuals that have never encountered the repellent. In addition, we show that a slime mould resulting from the fusion of a minority of habituated slime moulds and a majority of unhabituated ones still shows an adaptive response to the repellent. Finally, we further reveal that fusion must last a certain time to ensure an effective transfer of the behavioural adaptation between slime moulds. Our results provide strong experimental evidence that slime moulds exhibit transfer of learned behaviour during cell fusion and raise the possibility that similar phenomena may occur in other cell–cell fusion systems.
Multimodal single-cell analyses reveal distinct fusion-regulated transcriptional programs in Ewing sarcoma.
<p>All processed data for analysis at <a href="https://github.com/furlan-lab/EwS_multiome">https://github.com/furlan-lab/EwS_multiome</a></p>
Adoptive T Cell Therapy With DC/AML Fusion Vaccine Plus Decitabine and Venetoclax in AML
ClinicalTrials.gov study NCT07374029. IPD Sharing: YES. Countries: 1. Publications: 0.
A Phase 1 Study of Vaccination With Dendritic Cell (DC)/Multiple Myeloma (MM) Fusions in Combination With Elranatamab in Relapsed or Refractory Multiple Myeloma
ClinicalTrials.gov study NCT06799026. IPD Sharing: YES. Countries: 1. Publications: 0.
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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.