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37 results for “Proximity labeling”
Proximity labeling of tau interactions in primary neurons and mouse brain
<p><span>Microtubule-associated protein tau is a central factor in Alzheimer's disease and other tauopathies. However, physiological functions of tau are unclear. Here, we used proximity labelling proteomics to chart functional tau interactomes in primary neurons and mouse brai<span>n <span>in vivo</span></span><span>. Here, we use proximity labelling with the biotin ligase BioID2 to map interactomes of tau in neurons. Data sets relate to mass spectrometry and protein identification of biotinylated proteins in primary neurons and in mouse brain after delivery of BioID2-tau fusion protein or BioID2 control protein by adeno-associated virus (AAV). Mouse brain samples are either from P35 wild-type mice with intracranial AAV delivery at P0 or from tau knockout mice at P60 after hippocampal delivery of AAV. Details on BioID2 fusion protein expression, biotin supplementation and sample extraction can be obtained in the associated publication.<br></span></span></p>
Codes and source data files for: Proximity labeling identifies LOTUS domain proteins that promote the formation of perinuclear germ granules in C. elegans
<p>The germ line produces gametes that transmit genetic and epigenetic information to the next generation. Maintenance of germ cells and development of gametes require germ granules—well-conserved membraneless and RNA-rich organelles. The composition of germ granules is elusive owing to their dynamic nature and their exclusive expression in the germ line. Using <i>C. elegans</i> germ granule, called P granule, as a model system, we employed a proximity-based labeling method in combination with mass spectrometry to comprehensively define its protein components. This set of experiments identified over 200 proteins, many of which contain intrinsically disordered regions. An RNAi-based screen identified factors that are essential for P granule assembly, notably EGGD-1 and EGGD-2, two putative LOTUS-domain proteins. Loss of <i>eggd-1</i> and <i>eggd-2</i> results in separation of P granules from the nuclear envelope, germline atrophy and reduced fertility. We show that intrinsically disordered regions of EGGD-1 are required to anchor EGGD-1 to the nuclear periphery while its LOTUS domains are required to promote perinuclear localization of P granules. Together, our work expands the repertoire of P granule constituents and provides new insights into the role of LOTUS-domain proteins in germ granule organization.</p>
Proximity labeling of tau interactions in primary neurons and mouse brain
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Data from: Dynamics of the CD9 interactome during bacterial infection of epithelial cells by proximity labelling proteomics
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Codes and source data files for: Proximity labeling identifies LOTUS domain proteins that promote the formation of perinuclear germ granules in C. elegans
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Data from: Proximity-labeling proteomics reveals remodeled interactomes and altered localization of pathogenic SHP2 variants
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Proximity labeling-based profiling reveals a central role of the nuclear pore in mRNA metabolism
<p>The dataset for '<strong>Proximity labeling-based profiling reveals a central role of the nuclear pore in mRNA metabolism'</strong></p><p>This repository contains 81 high-confidence heterodimer complexes discussed in the publication. </p>
Data from: Proximity labeling reveals novel interactomes in live Drosophila tissue
Gametogenesis is dependent on intercellular communication facilitated by stable intercellular bridges connecting developing germ cells. During Drosophila oogenesis, intercellular bridges (referred to as ring canals) have a dynamic actin cytoskeleton that drives their expansion to a diameter of 10μm. While multiple proteins have been identified as components of ring canals (RCs), we lack a basic understanding of how RC proteins interact together to form and regulate the RC cytoskeleton. We optimized a procedure for proximity-dependent biotinylation in live tissue using the APEX enzyme to interrogate the RC interactome. APEX was fused to four different RC components (RC-APEX baits) and 55 unique high-confidence preys were identified. The RC-APEX baits produced almost entirely distinct interactomes that included both known RC proteins as well as uncharacterized proteins. The proximity ligation assay was used to validate close-proximity interactions between the RC-APEX baits and their respective preys. Further, an RNAi screen revealed functional roles for several high-confidence prey genes in RC biology. These findings highlight the utility of enzyme-catalyzed proximity labeling for protein interactome analysis in live tissue and expand our understanding of RC biology.
Scripts and Datasets for Photocatalytic Nanoscale Metal-Organic Framework for Proximity Labeling in Living Cells
<p>Please read data_process.ipynb for more details.</p>
Data from: Proximity labeling reveals novel interactomes in live Drosophila tissue
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Deep-Red and Ultrafast Photocatalytic Proximity Labeling Empowered in situ Dissection of Tumor-Immune Interactions in Primary Tissues
GEO Series GSE288148. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
Enzyme-mediated proximity labeling reveals the co-translational targeting of DLGAP5 mRNA to the centrosome during mitosis
GEO Series GSE260463. Homo sapiens. 14 samples. Type: Expression profiling by high throughput sequencing.
Mapping the FOXA1 Interactome in ER+ Breast Cancer Cells using Proximity Labeling Reveals Novel Interactions with the Orphan Nuclear Receptor NR2C2 [RNA-Seq]
GEO Series GSE299760. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
Proximity-dependent labeling identifies dendritic cells that prime the antitumor CD4+ T cell response
GEO Series GSE275471. Mus musculus. 857 samples. Type: Expression profiling by high throughput sequencing.
Time-Resolved Photocatalytic Proximity Labeling Uncovers ER Proteome Dynamics Underlying UPR to Apoptosis Transition [RNAseq_EMC2_knockdown]
GEO Series GSE298442. Homo sapiens. 8 samples. Type: Expression profiling by high throughput sequencing.
RNA proximity labeling in log phase Caulobacter crescentus NA1000
GEO Series GSE297938. Caulobacter vibrioides NA1000. 8 samples. Type: Expression profiling by high throughput sequencing.
In vivo proximity labeling and sequencing (IPL-seq) for SNRPN70 in 293T-Rex
GEO Series GSE55370. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing.
Time-Resolved Photocatalytic Proximity Labeling Uncovers ER Proteome Dynamics Underlying UPR to Apoptosis Transition [RNAseq_thapsigargin_treatment]
GEO Series GSE298441. Homo sapiens. 8 samples. Type: Expression profiling by high throughput sequencing.
Proximity RNA labeling by APEX-Seq Reveals the Organization of Translation Initiation Complexes and Repressive RNA Granules
GEO Series GSE121575. Homo sapiens. 37 samples. Type: Other.
Gene expression analysis and proximity labeling reveal posttranscriptional functions of the yeast RNA Polymerase II regulator Def1
GEO Series GSE290861. Saccharomyces cerevisiae. 40 samples. Type: Other; Expression profiling by high throughput sequencing.
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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.
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