Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
3,650
datasets available to search
ShareScore release 0.9.0
Dataset results
3,650 results for “antibody”
Dataset for the stimulator of interferon genes protein (STING1) antibody screening study
<p><strong>This antibody characterization dataset is related to the F1000 research article openly available at F1000Research.</strong></p> <p><em>This dataset contains the following underlying raw data for a study which characterized sixteen antibodies for the stimulator of interferon genes protein (STING1) in western blot, immunoprecipitation and immunofluorescence. The corresponding study is accessible on the YCharOS community on Zenodo (<a href="https://doi.org/10.5281/zenodo.11582350">https://doi.org/10.5281/zenodo.11582350</a>).</em></p> <p><em>The Dataset is in the format of a zip file. Once downloaded, please expand the zip file to access the folders containing the underlying data for Western blot (Wb), immunoprecipitation (IP) and immunofluorescence (IF).</em></p>
Dataset for the Fc receptor gamma-chain (FCER1G) antibody screening study
<p>This dataset contains the following underlying raw data for a study which characterized seven antibodies for the Fc receptor gamma chain (FCER1G) in western blot and immunoprecipitation. The corresponding study is openly accessible on the YCharOS community within Zenodo (DOI: 10.5281/zenodo.10845536).</p>
Dataset for the CSNK1A1 antibody screening study
<p><strong>This antibody characterization dataset is related to the F1000 research article openly available at F1000Research.</strong></p> <p><em>This Dataset contains the following underlying data for a study which evaluated ten CSNK1A1 antibodies by western blot, immunoprecipitation and immunofluorescence using a knockdown cell line as an isogenic control. The original study is also available on the Zenodo YCharOS community (<a href="https://doi.org/10.5281/zenodo.11618594">https://doi.org/10.5281/zenodo.11618594</a>).</em></p> <p><em>The Dataset is in the format of a zip file. Once downloaded, please expand the zip file to access the folders containing the underlying data for Western blot (Wb), immunoprecipitation (IP) and immunofluorescence (IF).</em></p>
Dataset for the Rab10 antibody screening study
<p><strong>This antibody characterization dataset is related to the F1000 research article openly available at F1000Research.</strong></p> <p>This Dataset contains the following underlying data for a study which evaluated eight Rab10 antibodies by western blot, immunoprecipitation and immunofluorescence using a knockdown cell line as an isogenic control. The original study is also available on the Zenodo YCharOS community (<a href="https://doi.org/10.5281/zenodo.13684961">https://doi.org/10.5281/zenodo.13684961</a>).</p> <p><em>The Dataset is in the format of a zip file. Once downloaded, please expand the zip file to access the folders containing the underlying data for Western blot (Wb), immunoprecipitation (IP) and immunofluorescence (IF).</em></p>
OMAP-23: Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of vermiform appendix (FFPE) with MICS on MACSima
<p><strong>Description</strong></p> <p> OMAP-23 was designed for MICS (MACSima imaging cyclic staining) imaging of FFPE human vermiform appendix sample. Tissue fixation and antigen retrieval is described in (<a href="https://www.biorxiv.org/content/biorxiv/early/2023/11/07/2023.10.27.564191.full.pdf">Spatial protein and RNA analysis on the same tissue section using MICS technology</a>). The MACSima technology is described in detail in the following publication (<a href="https://doi.org/10.1038/s41598-022-05841-4">MACSima imaging cyclic staining (MICS) technology reveals combinatorial target pairs for CAR T cell treatment of solid tumors</a>). All, antibodies in this panel are recombinant antibodies with a mutated human IgG1 constant region, removing Fc receptor binding capacity of human IgG1, eliminating the need for additional blocking steps and reducing non-specific binding. The use of human IgG1 recombinant antibodies allows for the addition of uncoupled monoclonal antibodies from other species followed by a fluorescence labelled secondary reagent specific for the species of the monoclonal antibody. The multiplex system has been described already for OMAP-10 and OMAP-21. A new dye VioB515 is used for one reagents. The fluorescence is removed by cleavage. The panel contains 28 antibodies and the nuclear marker DAPI for image alignment and nuclear segmentation. This OMAP provides a spatial context for six anatomical structures and most cell types present in the vermiform appendix (link to ASCT+B table added). OMAP-23 follows OMAP-21, with fewer antibodies but adding antibodies for non-immune cells.</p> <p>All reagents are from Miltenyi Biotec and have been rigorously tested through an internal quality control system to have minimal variation between lots. For this reason, lot information is not included in this table. Analysis was performed by an accompanied software package MACSIQ View Analysis also described in the MACSima publication (<a href="https://doi.org/10.1038/s41598-022-05841-4">https://doi.org/10.1038/s41598-022-05841-4</a>). The MACSima system is continuously evolving, this is the third OMAP for the MACSima system. A representative dataset created using OMAP-23 can be found here 10.5281/zenodo.14008816 .The AVRs for the dataset can be found here (to be added).</p>
A vaccine-induced public antibody protects against SARS-CoV-2 and emerging variants
<p>These are the<strong> processed</strong> BCR repertoire bulk sequencing data described in <a href="https://doi.org/10.1016/j.immuni.2021.08.013">Schmitz, Turner & Liu et al., Immunity, 2021</a>. The <strong>raw</strong> sequence data are available on SRA under BioProjects <a href="https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA731610">PRJNA731610</a> and <a href="https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA741267">PRJNA741267</a>. </p> <p><strong>Summary</strong>: Bulk-sorted total plasmablasts and IgDlo enriched B cells from PBMCs and germinal centre B cells from lymph nodes from various timepoints after primary immunization from 22 BNT162b2 vaccinees who had no prior history of infection with SARS-CoV-2. </p> <p><strong>Metadata file</strong>: WU368_schmitz_et_al_immunity_2021_meta.tsv</p> <p>Abbreviations:</p> <ul> <li>LN = lymph node</li> <li>PB = plasmablast</li> <li>GC = germinal center</li> <li>mAb = monoclonal antibody</li> </ul> <p><strong>BCR data file</strong>: WU368_schmitz_et_al_immunity_2021_bcr.tsv.gz</p> <p>In addition to the processed bulk sequences, also included are the heavy chains of 37 mAbs (including 2C08) first reported in <a href="https://doi.org/10.1038/s41586-021-03738-2">Turner & O'Halloran et al., Nature, 2021</a> that had been validated to be spike-binding. The mAbs are annotated as "mab" in the "seq_type" column.</p> <p><strong>Sequence data column description</strong></p> <p>The columns largely follow the <a href="https://changeo.readthedocs.io/en/stable/standard.html">AIRR-C Rearrangement format</a>. The main deviation is that CDR3s are used, as opposed to IMGT-defined "junctions". Non-standard columns are noted below.</p> <ul> <li>v_call_genotyped: V gene annotation reassigned after individualized genotyping by <a href="https://tigger.readthedocs.io/en/stable/">TIgGER</a></li> <li>isotype: IGH[ADEGM]</li> <li>cdr3: CDR3 nucleotide sequence</li> <li>cdr3_length: CDR3 nucleotide sequence length</li> <li>cdr3_aa: CDR3 amino acid sequence</li> <li>donor: vaccinee ID</li> <li>sample: sample ID (arbitrary)</li> <li>timepoint: time point at which sample was collected</li> <li>tissue: tissue from which sample was collected</li> <li>sorting: FACS sorting</li> <li>seq_type: sequence type (mAb or bulk)</li> </ul>
A common NFKB1 variant detected through antibody analysis in UK Biobank predicts risk of infection and allergy: Summary statistics - Health records
<p>Infectious agents contribute significantly to the global burden of diseases, through both acute infection and their chronic sequelae. We leveraged the UK Biobank to identify genetic loci that influence humoral immune response to multiple infections. From 45 genome-wide association studies in 9,611 participants from UK Biobank, we identified NFKB1 as a locus associated with quantitative antibody responses to multiple pathogens including those from the herpes, retro- and polyoma-virus families. An insertion-deletion variant thought to affect NFKB1 expression (rs28362491), was mapped as the likely causal variant. This variant has persisted throughout hominid evolution and could play a key role in regulation of the immune response. Using 121 infection and inflammation related traits in 487,297 UK Biobank participants, we show that the deletion allele was associated with an increased risk of infection from diverse pathogens but had a protective effect against allergic disease. We propose that altered expression of NFKB1, as a result of the deletion, modulates haematopoietic pathways, and likely impacts cell survival, antibody production, and inflammation. Taken together, we show that disruptions to the tightly regulated immune processes may tip the balance between exacerbated immune responses and allergy, or increased risk of infection and impaired resolution of inflammation. </p> <p>-------------------------------------------------------------------------------------</p> <p>This dataset contains GWAS summary statistics for infection, inflammation, and allergy related traits in 487,297 individuals</p>
A common NFKB1 variant detected through antibody analysis in UK Biobank predicts risk of infection and allergy: Summary statistics - Serology
<p>Infectious agents contribute significantly to the global burden of diseases, through both acute infection and their chronic sequelae. We leveraged the UK Biobank to identify genetic loci that influence humoral immune response to multiple infections. From 45 genome-wide association studies in 9,611 participants from UK Biobank, we identified NFKB1 as a locus associated with quantitative antibody responses to multiple pathogens including those from the herpes, retro- and polyoma-virus families. An insertion-deletion variant thought to affect NFKB1 expression (rs28362491), was mapped as the likely causal variant. This variant has persisted throughout hominid evolution and could play a key role in regulation of the immune response. Using 121 infection and inflammation related traits in 487,297 UK Biobank participants, we show that the deletion allele was associated with an increased risk of infection from diverse pathogens but had a protective effect against allergic disease. We propose that altered expression of NFKB1, as a result of the deletion, modulates haematopoietic pathways, and likely impacts cell survival, antibody production, and inflammation. Taken together, we show that disruptions to the tightly regulated immune processes may tip the balance between exacerbated immune responses and allergy, or increased risk of infection and impaired resolution of inflammation. </p> <p>-------------------------------------------------------------------------------------</p> <p>This dataset contains GWAS summary statistics for quantitative antibody responses in 9611 individuals and results for a meta-analysis of UK Biobank and CoLaus/PsyCoLaus antibody responses.</p> <p> </p>
Antibody landscape of C57BL/6 mice cured of B78 melanoma via immunotherapy
<p>Antibodies can play an important role in innate and adaptive immune responses against cancer, and in preventing infectious disease. Using a Nimble Therapeutics high-density peptide array, we assessed potential protein-targets for antibodies found in sera of immune mice, that were previously cured of their melanoma through a combined immunotherapy regimen with long-term memory. Using flow cytometry, immune sera showed strong antibody-binding against melanoma tumor cell lines. Sera from 6 of these cured mice were analyzed with this high-density, whole-proteome peptide-array to determine specific antibody-binding sites and their linear peptide sequence. We identified thousands of peptides that were targeted by 2 or more of these 6 mice and exhibited strong antibody binding only by immune, not naive sera. Confirmatory studies were done to validate these results using 2 separate ELISA-based systems. This technology may be helpful in studying the “immunome”. of protein-based epitopes that are recognized by immune sera from mice, or possibly patients, cured of cancer via immunotherapy.</p>
OMAP-10: Multiplexed Antibody-Based Imaging of Human Palatine Tonsil with MACSima v1.0
<p> </p> <p>OMAP-10 was designed for MACSima (MACSima imaging cyclic staining) imaging of <em>paraformaldehyde</em> (PFA)-fixed human tonsil samples. The MACSima technology is described in detail in the following publication (<a href="https://doi.org/10.1038/s41598-022-05841-4">https://doi.org/10.1038/s41598-022-05841-4</a>). Most, but not all, antibodies in this panel are recombinant antibodies with a mutated human IgG1 constant region. The described mutation removes the Fc receptor binding capacity of human IgG1, eliminating the need for additional blocking steps and reducing non-specific binding of human antibodies on human tissues. Highly multiplexed imaging is achieved through cycles of immunolabeling with FITC, PE, and APC conjugated antibodies and photobleaching to eliminate fluorescence signal between imaging cycles. The panel contains 30 antibodies and the nuclear marker DAPI for image alignment and nuclear segmentation. This OMAP provides a spatial context for all anatomical structures and most cell types present in the ASCT+B tonsil table, v1.0 (submitted for review). OMAP-10 follows closely OMAP-1 described for human lymph nodes (<a href="https://hubmapconsortium.github.io/ccf-releases/v1.3/docs/omap/omap-1-human-lymph-node-ibex.html">https://hubmapconsortium.github.io/ccf-releases/v1.3/docs/omap/omap-1-human-lymph-node-ibex.html</a>). The initial dataset associated with OMAP-10 can be found in this dataset. All reagents were obtained from Miltenyi Biotec and have been rigorously tested through an internal quality control system to have minimal variation between lots. For this reason, lot information is not included in the table below. Analysis was performed by an accompanied software package MACSIQ View Analysis also described in the MACSima publication (<a href="https://doi.org/10.1038/s41598-022-05841-4">https://doi.org/10.1038/s41598-022-05841-4</a>). The plan was to also include the data analysis in the uploaded dataset. However mixing the original data with analyses data would lead to confusion. Therefore only the original image files are included here. This is in brief the image analysis pipeline: the software processes the raw images of the MACSima run, generates stitched images, and then allows downstream analysis including cell segmentation, cell gating, data normalization, dimension reduction plots (tSNE, UMAP), heat maps, distance analyses and cluster analyses, all of which are interactively linked together. The MACSima system is continuously evolving, and this is the first OMAP dataset generated by using the MACSima system (Instrument, Reagents and Software).</p> <p>The images enclosed are in OME-tif format (16 bit depth). The optical resolution is 0.17 micron/pixel. The imaged area size is 1.6 mm x 1.3 mm. This Data is currently under review by the OMAP community and changes are still possible in the follow up version. The image contains stichted images of 9 fields of view. The complete runtime on the MACSima for this image dataset was about 12 hours on the instrument. The OMAP description also links to the ASCT+B table for the palatine tonsil.</p> <p><strong>Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) table for Palatine Tonsil v1.0</strong></p> <p><strong>Description</strong></p> <p><a href="https://hubmapconsortium.github.io/ccf/pages/ccf-anatomical-structures.html">Anatomical Structures, Cell Types, plus Biomarkers (ASCT+B) tables</a> aim to capture the nested <em>part of</em> structure of anatomical human body parts, the typology of cells, and biomarkers used to identify cell types. The tables are authored and reviewed by an international team of experts. The Palatine Tonsil ASCT+B table is derived from published literature, public datasets, and unpublished studies from table authors. The Palatine Tonsil is part of the tonsiluar ring of Waldeyer network. In comparison to other Tonsils the Palatine Tonsil has an enlarged lymphoid tissue.</p> <p>The gene biomarkers are primarily derived from a preprint on an Atlas of Cells of the human tonsil (<a href="https://www.biorxiv.org/content/10.1101/2022.06.24.497299v1">Ramon Massoni-Badosa et al 2022</a>). The tonsil azimuth data set can be explored <a href="https://azimuth.hubmapconsortium.org/references/human_tonsil/">here</a> .Cell phenotypes, especially for antibody-based assays like the MACSima are very complex and in its first version, only the basic cell types are listed with many more to be included in the next iteration of the ASCT+B table. The correlation between protein detection and RNA expression data at the single cell level needs to be established. In total, this table reports 13 anatomical structures, 17 cell types, and 30 biomarkers. </p> <p>The following list contains the file name and the target name of the antibody used in a given staining:</p> <p>ACTIN_REAL650/ACTA2</p> <p>Bcl2_REA872/BCL2</p> <p>CD11c_REAL235/ITGAX</p> <p>CD138_REA929/SDC1</p> <p>CD15_VIMC6/FUT4</p> <p>CD19_REAL106/CD19</p> <p>CD1c_REA694/CD1C</p> <p>CD209_REAL1087/CD209</p> <p>CD20_REA1087/MS4A1</p> <p>CD21_REA940/CR2</p> <p>CD274_PDL1/CD274</p> <p>CD279_REAL531/PDCD1</p> <p>CD27_REA499/CD27</p> <p>CD39_REA739/ENTPD1</p> <p>CD3_REAL1097/CD3E</p> <p>CD44_REA690/CD44</p> <p>CD4_REA1307/CD4</p> <p>CD68_REA1306/CD68</p> <p>CD79a_REA1142/CD79A</p> <p>CD8_REA734/CD8A</p> <p>CollagenIV_REAL1212/COL4A1</p> <p>Cytokeratin_CK36H5/KRT7,KRT8,KRT18,KRT19</p> <p>FoxP3_REA1253/FOXP3</p> <p>HLADR_REAL550/HLA-DRA</p> <p>IgD_REA740/IGHD</p> <p>IgM_REAL689/IGHM</p> <p>Ki67_REA183/MKI67</p> <p>PlasmaCell_REA908/CKAP4</p> <p>Vimentin_REA409/VIM</p>
Multiplexed Staining Dataset - OMAP 5 - Liver-Lanthanides-conjugated antibodies and C60-secondary ion mass spectrometry imaging
<p>This dataset contains images of multiplexed antibody panel on a human pediatric liver section including the nuclear marker and antibodies conjugated with lanthanides tags. The dataset is one example of serial experiments of multiplexed antibody staining and imaging. The antibody panel targets the major cell types and tissue structures in the liver tissue. Data acquisition was performed using single multiplexing imaging by C60-secondary ion mass spectrometry.</p> <p> </p>
Mass spectrometry output SILAC labelled (F/Y) biological replicate 1 - anti-HLA-A29 antibody DK1G8
<p>Mass spectrometry output from SILAC labelled (F/Y) ERAP2 wildetype versus (CRISPR Cas9-mediated) ERAP2-KO lymphoblastoid cell line from a Birdshot Uveitis patient (ERAP1 hap10/10 ERAP2 hapA/A). Peptides were eluted from immuno-purifications with anti-HLA-A29 antibody DK1G8. The dataset was used for subsequent filtering and differential expression analysis by <em>limma</em>. </p>
Data from: Blockade of dengue virus transmission from viremic blood to Aedes aegypti mosquitoes using human monoclonal antibodies
Background <p class="CxSpFirst">Dengue is the most prevalent arboviral disease of humans. Virus neutralizing antibodies are likely to be critical for clinical immunity after vaccination or natural infection. A number of human monoclonal antibodies (mAbs) have previously been characterized as able to neutralize the infectivity of dengue virus (DENV) for mammalian cells in cell-culture systems.</p> <p class="CxSpLast"> </p> Methodology/Principle findings <p class="CxSpFirst">We tested the capacity of 12 human mAbs, each of which had previously been shown to neutralize DENV in cell-culture systems, to abrogate the infectiousness of dengue patient viremic blood for mosquitoes. Seven of the twelve mAbs (1F4, 14c10, 2D22, 1L12, 5J7, 747(4)B7, 753(3)C10), almost all of which target quaternary epitopes, inhibited DENV infection of <i>Ae. aegypti</i>. The mAbs 14c10, 747(4)B7 and 753(3)C10 could all inhibit transmission of DENV in low microgram per mL concentrations. An Fc-disabled variant of 14c10 was as potent as its parent mAb.</p> <p class="CxSpLast"> </p> Conclusions/Significance <p class="CxSpFirst">The results demonstrate that mAbs can neutralize infectious DENV derived from infected human cells, in the matrix of human blood. Coupled with previous evidence of their ability to prevent DENV infection of mammalian cells, such mAbs could be considered attractive antibody classes to elicit with dengue vaccines, or alternatively, for consideration as therapeutic candidates.</p>
Data from: Natural selection on antihelminth antibodies in a wild mammal population
<p>An effective immune response is expected to confer fitness benefits through improved resistance to parasites but also energetic costs which negatively impact fitness-related traits such as reproduction. These fitness costs and benefits of an immune response are likely to depend on host age, sex, and levels of parasite exposure. Few studies have examined the full extent to which patterns of natural selection on immune phenotypes vary across demographic groups and environments in the wild. Here, we assessed natural selection on plasma levels of three functionally distinct isotypes (IgA, IgE and IgG) of antibodies against a prevalent nematode parasite measured in a wild Soay sheep population over 25 years. We found little support for environment-dependent selection or reproductive costs. However, antibody levels were negatively associated with parasite egg counts and positively associated with subsequent survival, albeit in a highly age- and isotype-dependent manner. Raised levels of anti-parasite IgA best predicted reduced egg counts but this did not predict survival in lambs, whilst in adult females increased anti-parasite IgG predicted reduced egg counts and improved survival. Our results highlight the potential importance of age-dependent selection on immune phenotypes in nature, and that patterns of selection can vary even amongst functionally-related immune markers.</p>
Naive B cells, Antibody secreting cells, Plasma cells
<p>Raw Illumina MiSeq data in zipped FASTQ format. The data set includes demultiplexed samples from naive B cells (_20433_), antibody secreting cells (_20434_) and plasma cells (_20435_) obtained from the same Balb/c mouse via sorting. Every sample consists of forward (_R1_), reverse (_R2_) reads (2x250 bp).</p>
A Chinese female Morvan patient with LGI1 and CASPR2 antibodies: a case report
<p>Figure 1-2 of the case and the original photos under fluorescence microscope. Fig. 1 Cranial MRI of our patient. Fig. 2 The immunoreactivity of patient’s serum to CASPR2 and LGI1 proteins.</p>
Simulations from "Mechanistic computational modeling of monospecific and bispecific antibodies targeting interleukin-6/8 receptors"
<h1>IL6R/IL8R Antibody Binding Model Code</h1> <p>Christina M.P. Ray, Huilin Yang, Jamie B. Spangler, Feilim Mac Gabhann</p> <p>This dataset contains all simulation output files generated for the article "Mechanistic computational modeling of monospecific and bispecific antibodies targeting interleukin-6/8 receptors". The model is comprised of a coupled set of ordinary differential equations (ODEs) where each individual ODE describes one molecule (antibody or receptor) or molecular complex (antibody + receptor). The terms in the ODEs represent each binding interaction (binding and unbinding processes) in the system.</p> <p>The code for the binding model and for the analysis and visualization results is available on GitHub at <a href="https://github.com/christyray/bispecific-binding-model">christyray/bispecific-binding-model</a>.</p> <h2>Specific Simulations</h2> <p>The <code>.csv</code> and <code>.rds</code> files in the correspond to the results from the simulations performed for the article "Mechanistic computational modeling of monospecific and bispecific antibodies targeting interleukin-6/8 receptors". These files can be read into R using the <code>import_data()</code> function included in the <a href="https://github.com/christyray/bispecific-binding-model">GitHub repository</a>.</p> <p>The <code>id</code> files contain simulation IDs to link the molecule concentrations (<code>yin</code>) and parameter values (<code>params</code>) with the simulation results (<code>out</code>). When applicable, the <code>norm</code> files contain normalized simulation output, and the <code>occupied</code> files contain receptor fractional occupancy values calculated from the simulation output.</p> <ul> <li><code>optimization</code>: Optimization of binding rate constants (association and dissociation) to experimental <em>in vitro</em> flow cytometry data; results displayed in Figure 2</li> <li><code>binding-curve</code>: Model simulations using the best-fit parameter set for comparison to the experimental data used to fit the model parameters; results displayed in Figure 3</li> <li><code>compare-opt</code>: Model simulations using each of the optimized parameter sets; results displayed in the Supplemental Information</li> <li><code>time</code>: Simulations of antibody binding dynamics over time; results displayed in Figure 4</li> <li><code>concentration</code>: Simulations with varying antibody concentrations and receptor expression levels; results displayed in Figure 5</li> <li><code>monovalent</code>: Simulations restricted to monovalent antibody binding only; results displayed in Figure 6</li> <li><code>compare-ab</code> and <code>compare-recep</code>: Simulations of both the bispecific antibody BS1 and the combination of monospecific antibodies tocilizumab and 10H2 for comparsion; results displayed in Figure 7</li> <li><code>local</code> and <code>global</code>: Local and global univariate sensitivity analyses; results displayed in Figure 8</li> </ul> <h2>References</h2> <blockquote> <p>H. Yang, M. N. Karl, W. Wang, B. Starich, H. Tan, A. Kiemen, A. B. Pucsek, Y.-H. Kuo, G. C. Russo, T. Pan, E. M. Jaffee, E. J. Fertig, D. Wirtz, and J. B. Spangler. Engineered bispecific antibodies targeting the interleukin-6 and -8 receptors potently inhibit cancer cell migration and tumor metastasis. Molecular Therapy, 30(11):3430–3449, Nov. 2022. doi:<a href="https://doi.org/10.1016/j.ymthe.2022.07.008">10.1016/j.ymthe.2022.07.008</a></p> </blockquote>
OMAP-8: Multiplexed Antibody-Based Imaging of Placenta with Imaging Mass Cytometry (IMC), v1.0
<p>OMAP-8 was designed for Imaging Mass Cytometry (IMC) (<a href="https://pubmed.ncbi.nlm.nih.gov/24584193/">https://pubmed.ncbi.nlm.nih.gov/24584193/</a>) of formalin-fixed paraffin-embedded (FFPE) human term-placenta samples. The tissue slides were prepared with a two-step antigen retrieval process (pH 6 and pH 9, as described <a href="https://dx.doi.org/10.17504/protocols.io.bpwumpew">https://dx.doi.org/10.17504/protocols.io.bpwumpew</a>). OMAP antibodies validated by immunohistochemistry and IMC were conjugated to polymers containing metal isotopes. Conjugated antibodies were used to stain processed human term-placenta tissue simultaneously. Regions of the processed tissue were then acquired on the imaging mass cytometer (Hyperion; Standard BioTools) by laser ablation and visualized. The panel contains 26 antibodies conjugated to unique metal isotopes and iridium marks the DNA. This OMAP provides a spatial context for key placenta cell types in the <a href="https://doi.org/10.48539/HBM446.WGLG.755">ASCT+B v.1.0 table</a>. Single-cell RNA sequencing data were used to guide marker selection for multiplexed tissue imaging. For example, ASCL2, HLA-G, PD-L1, CD68 and LYVE1 allow functionally specialized cell types to be visualized and quantified in the placenta. Note that one of our core antibodies is to LYVE1 but, unlike in other tissues where it is used to mark lymphatic vasculature, here we use it to mark the macrophage of the placenta (Hofbauer cells) – there should be no lymphatics in the placenta.</p>
Raw diffraction images of the crystal structure of human VISTA extra cellular domain in complex with Fab fragment of pH-selective anti-VISTA antibody
<p>The diffraction datasets was collected at X10SA, SLS. The dataset was collected from one crystal using a rotation scheme for 222º oscillation with the following experimental parameters; Wavelength: 0.9998 Å, Detector: EIGER2 Si 16M (DECTRIS Co. Ltd.). The crystal belonged to space group C 1 2 1 with unit cell parameters a=207.66, b=39.51, c=177.98 Å, and beta=117.12°.</p><p>PDB ID: 8TBQ</p>
Self-Assembled Proteomimetic (SAP) with Antibody-like Binding from Short PNA-Peptide Conjugates
<p><span><span>Affinity proteins </span><span>based on </span><span>a </span><span>three-helix </span><span>bundle</span> <span>(</span><span>affibodies, </span><span>alphabodies</span><span> and computationally </span></span><span><span>de novo</span></span><span> <span>designed</span><span> ones)</span><span> have shown to be a general platform to discover binders with properties reminiscent of </span><span>antibodies</span><span>, combining </span><span>high </span><span>target </span><span>specificity</span><span> with </span><span>affinities reaching well below</span> <span>the </span><span>nanomolar</span><span>.</span> <span>Herein</span><span>,</span><span> we report a new strategy</span><span>, coined self-assembled proteomimetic (SAP)</span><span>,</span><span> to mimic </span><span>such</span><span> three-helix bundle</span><span> architecture with a hybridization-enforced two-helix </span><span>coiled</span> <span>coil</span><span> that is obtained by templated</span> <span>native chemical ligation (</span><span>T-</span><span>NCL) of PNA-peptide conjugates.</span> <span>This SAP </span><span>strategy</span> <span>stands out by</span><span> its</span><span> synthetic accessibility reducing the length on the longest </span><span>synthetic</span><span> peptide to </span><span>less than 30 amino acids, readily attainable by standard SPPS methodologies</span><span>. We show that the </span><span>T</span><span>-NCL dramatically accelerates the </span><span>ligation</span><span>, enabling this chemistry to </span><span>proceed</span> <span>in a combinatorial fashion </span><span>at</span><span> low</span> <span>micromolar</span><span> concentration</span><span>s</span><span>.</span> <span>We </span><span>demonstrate</span> <span>that small </span><span>combinatorial </span><span>libraries of </span><span>SAP</span><span>s</span><span> can be prepared in one operation and used directly in </span><span>affinity selection</span><span>s</span><span> against a target of interest </span><span>with an</span><span> LC-MS </span><span>analysis</span><span> of the fittest binders</span><span>.</span> <span>Moreover, we </span><span>show</span><span> that </span><span>the underlying</span> <span>design</span><span> paradigm</span><span> is functional for</span><span> SAPs based on structurally distinct three-helix peptides </span><span>aimed at</span><span> different </span><span>therapeutic </span><span>targets, namely</span> <span>HER2 </span><span>and</span><span> spike’s RBD</span><span>,</span></span> <span><span>reaching picomolar </span><span>affinities</span></span><span><span>. We further </span><span>illustrate </span><span>that the</span> <span>affinity </span><span>of the </span><span>S</span><span>AP</span><span> can be allosterically regulated using a toehold displacement</span><span> of the hybridizing PNAs</span><span> to disrupt the </span><span>coiled coil</span><span> stabilization.</span> <span>Finally, w</span><span>e show that </span><span>an RBD-targeting </span><span>SAP effectively inhibits viral </span><span>entry </span><span>of SARS-CoV-2</span> <span>with an IC</span></span><span><span>50</span></span><span><span> of </span><span>2.8</span> <span>nM</span><span>.</span></span><span> </span></p>
ScienceDex guides
Understand access before you commit
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.