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Dataset results
60 results for “nanobodies”
INSPIRE-seq simultaneously selects nanobodies for immune epitopes in the complex tumor microenvironment
<p>scRNAseq of CD45 magnetic microbeads enriched cells were isolated form Py8119 bearing mice (three mice per pool/group) two hours after injection of either PBS, insertless phage display, CD45, DCs, or CD8 specific VHHs phage display libraries. </p>
Study to Assess Efficacy and Safety of Anti-von Willebrand Factor (vWF) Nanobody in Patients With Acquired Thrombotic Thrombocytopenic Purpura (aTTP)
ClinicalTrials.gov study NCT01151423. IPD Sharing: YES. Countries: 13. Publications: 3.
Engineering of Nanobodies recognizing the human chemokine receptor CCR7
<p>raw data of each figure published in 10.3390/ijms20102597 (Engineering of Nanobodies Recognizing the Human Chemokine Receptor CCR7)</p>
ESAT-6 undergoes self-association at phagosomal pH and an ESAT-6 specific nanobody restricts M. tuberculosis growth in macrophages
<p><em>Mycobacterium tuberculosis</em> (Mtb) is known to survive within macrophages by compromising the integrity of the phagosomal compartment in which it resides. This activity primarily relies on the ESX-1 secretion system, predominantly involving the protein duo ESAT-6 and CFP-10. CFP-10 likely acts as a chaperone, while ESAT-6 likely disrupts phagosomal membrane stability via a largely unknown mechanism. we employ a series of biochemical analyses, protein modeling techniques, and a novel ESAT-6-specific nanobody to gain insight into the ESAT-6’s mode of action. First, we measure the binding kinetics of the tight 1:1 complex formed by ESAT-6 and CFP-10 at neutral pH. Subsequently, we demonstrate a rapid self-association of ESAT-6 into large complexes under acidic conditions, leading to the identification of a stable tetrameric ESAT-6 species. Using molecular dynamics simulations, we pinpoint the most probable interaction interface. Furthermore, we show that cytoplasmic expression of an anti-ESAT-6 nanobody blocks Mtb replication, thereby underlining the pivotal role of ESAT-6 in intracellular survival. Together, these data suggest that ESAT-6 acts by a pH dependent mechanism to establish two-way communication between the cytoplasm and the Mtb-containing phagosome.</p>
X-ray diffraction dataset for the complex between CNPase and nanobody 5E
<p>Raw diffraction data for the crystal structure between mouse CNPase catalytic domain and anti-CNPase nanobody 5E.</p>
X-ray diffraction data for CNPase bound to nanobody 8C
<p>X-ray diffraction dataset for complex between mouse CNPase catalytic domain and anti-CNPase nanobody 8C</p>
X-ray diffraction data for the complex between CNPase and nanobody 7E
<p>X-ray diffraction dataset for the complex between mouse CNPase catalytic domain and nanobody 7E. </p>
X-ray diffraction data for the complex between CNPase and nanobody 10E
<p>X-ray diffraction dataset for the complex between mouse CNPase catalytic domain and anti-CNPase nanobody 10E</p>
Huntingtin intrabody and nanobody literature review 10th January 2018
<p>Huntingtin structure-function open lab notebook project. </p> <p>To kick off the new year, I have been doing some reading on huntingtin intrabodies and nanobodies and have written this up into an informal literature review. These are small Ig domain proteins which specifically bind different regions of huntingtin. All of those which I have written about, bind the exon 1 of huntingtin, some with specificity for the N17 region, whereas others bind the polyproline or proline rich domains.</p> <p>Thanks to Prof Ray Truant, who kindly provided me with some nanobody clones, I have already expressed and purified iVHH4. I plan to clone, express and purify Happ1 and VL12.3, both of which are single Ig domain proteins, and along with iVHH4, test binding to my huntingtin protein samples and see if they help stabilize my samples.</p> <p>http://labscribbles.com/2018/01/10/huntingtin-intrabody-and-nanobody-literature-review/ </p>
Huntingtin nanobody purification using osmotic shock cell lysis and growth in M9 media – 2018/04/09
<p>Huntingtin structure-function open lab notebook project. Huntingtin nanobody purification using osmotic shock cell lysis and growth in M9 media – 2018/04/09</p>
Huntingtin nanobody purification using osmotic shock cell lysis – 2018/04/02
<p>Huntingtin structure-function open lab notebook project. Huntingtin nanobody purification using osmotic shock cell lysis – 2018/04/02.</p>
The use of nanobodies in a sensitive ELISA test for SARS-CoV-2 Spike 1 protein
<p>A rapid detection method for SARS-CoV-2 spike protein is essential for control of COVID19. We investigated various combinations of engineered nanobodies in a sandwich ELISA to detect the Spike protein of SARS-CoV-2. We have identified an optimal combination of nanobodies. These were selectively functionalised to further improve antigen capture. This dataset contains data from ELISA experiments described in the manuscript.<span> </span></p> <p><span>Plate coating of nanobodies for ELISA by passive adsorption vs biotinylation was compared. A series of nanobody pairings (two cluster 2 ACE2-binding epitope and two cluster 1 CR3022 epitope) were screened for optimum sensitivity. The optimal pair were then tested against a series of SARS-COV-2 antigens: recombinant spike 1 protein; recombinant receceptor binding domain (RBD); pseudotyped HIV-1 and heat-empigen inactivated SARS-CoV-2 virus. X-ray irradiated SARS-CoV-2 was also tested. Sensitivity to these antigens was compared with nanobodies biotinylated a) site-selectively and b) in a non-specific stochastic manner. Batch-to-batch viral variation and effects of inactivating agents were investigated. Limit of detection was compared against delta and beta viral mutants. Combining optimal nanobody pairing and site-selective biotinylation, we observed a limit of detection of 147 pg/mL for Spike protein; 33 pg/mL for RBD; 16 TCID50/mL of pseudovirus and 15 ffu/mL of heat-Empigen inactivated SARS-CoV-2. The pairing also showed sensitivity towards delta variant. We have demonstrated the use and sensitivity of nanobodies in ELISA by detection of recombinant and viral SARS-CoV-2 antigens.</span></p>
Mass Spectrometry Datasets for "Highly synergistic combinations of nanobodies that target SARS-CoV-2 and are resistant to escape"
<p>This repository contains mass spectrometry raw datasets for the research paper "<strong><em>Highly synergistic combinations of nanobodies that target SARS-CoV-2 and are resistant to escape</em></strong>". An early version of the manuscript can be viewed on <a href="https://www.biorxiv.org/content/10.1101/2021.04.08.438911v1">bioRxiv</a>.</p> <p>The datasets include two parts:</p> <ol> <li>Identification of nanobodies targeting SARS-CoV-2 spikes.</li> <li>Chemical cross-linking of nanobody-spikes complexes.</li> </ol> <p>The included <strong>.raw</strong> files are Thermo Orbitrap Raw files, and can be assessed by various software such as <em>Thermo Xcalibur</em>, <em><a href="https://proteowizard.sourceforge.io/">ProteoWizard</a></em> and <em><a href="https://pypi.org/project/pymsfilereader/">pymsfilereader</a></em>.</p>
The use of nanobodies in a sensitive ELISA test for SARS-CoV-2 Spike 1 protein
Open the record for dataset details and reuse information.
DSMBind: SE(3) denoising score matching for unsupervised binding energy prediction and nanobody design
<p>This record provides the training and evaluation dataset for DSMBind</p> <p>Paper link: https://www.biorxiv.org/content/10.1101/2023.12.10.570461v1.abstract</p> <p>Github repo: https://github.com/wengong-jin/DSMBind</p>
HTT Nanobody Test Expression and Purification 2017/10/12
<p>Huntingtin structure function open lab notebook project</p>
Expression and purification of huntingtin nanobody iVHH4 in E. coli (2017/11/20)
<p>Huntingtin structure function open lab notebook</p>
ITC data set of nanobody (Nb33) binding to PaaR2 repressor truncates from Escherichia coli O157:H7
<p>Raw isothermal titration calorimetry data set from the published article De Bruyn, P., Prolič-Kalinšek, M., Vandervelde, A., Malfait, M., Sterckx, Y. G. J., Sobott, F., Hadži, S., Pardon, E., Steyaert, J., & Loris, R. (2021). Nanobody-aided crystallization of the transcription regulator PaaR2 from Escherichia coli O157:H7. <em>Acta crystallographica. Section F, Structural biology communications</em>, <em>77</em>(Pt 10), 374–384. https://doi.org/10.1107/S2053230X21009006.</p> <p>Titrations were measured at different temperatures (5-37 °C, indicated in the file name). Concentrations are listed in each itc data file. Buffer is 10 m<em>M</em> NaH<sub>2</sub>PO<sub>4</sub>, 10 m<em>M</em> Na<sub>2</sub>HPO<sub>4</sub>, 150 m<em>M</em> NaCl, 0.01% Triton X-100, pH 7.5.</p>
PD-L1 Targeting Nanobody Probe for PET Imaging of Solid Tumor
ClinicalTrials.gov study NCT05156515. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Nanobody-based Biepitope CAR-T Cells Targeting BCMA in the Treatment of R/RMM
ClinicalTrials.gov study NCT06503107. IPD Sharing: Not stated. Countries: 1. Publications: 4.
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.