Find research datasets worth reusing

opencc-by-4.0Nov 2020View details →

The Clinical Significance of Serum p53 Antibody Levels in Patients with Oral Squamous Cell Carcinoma in Japanese Clinical Practice

Supplementary Figure S1. Serum anti-p53 antibody titers in each clinical stage. Supplementary Table S1. The change of Ap53Ab titer in patients  with OSCC after surgery.

opencc-zeroFeb 2020View details →

Immunization with full-length Plasmodium falciparum merozoite surface protein 1 is safe and elicits functional cytophilic antibodies in a randomized first-in-human trial

This file contains the original data underpinning the article in npj vaccines, in which we describe a phase 1 safety and immunogenicty study on the malaria vaccine candidate MSP1 in humans. The abstract of the article follows: A vaccine remains a priority in the global fight against malaria. Here, we report on a single-center, randomized, double-blind, placebo and adjuvant-controlled, dose escalation phase 1a safety and immunogenicity clinical trial of full-length Plasmodium falciparum merozoite surface protein 1 (MSP1) in combination with GLA-SE adjuvant. 32 healthy volunteers were vaccinated at least three times with MSP1 plus adjuvant, adjuvant alone or placebo (24:4:4) to evaluate the safety and immunogenicity. MSP1 was safe, well tolerated and immunogenic, with all vaccinees sero-converting independent of the dose. The MSP1-specific IgG and IgM titers persisted above levels found in malaria semi-immune humans for at least six months after the last immunization. The antibodies were variant- and strain-transcending and stimulated respiratory activity in granulocytes. Furthermore, full-length MSP1 induced memory T-cells. Our findings encourage challenge studies as the next step to evaluate the efficacy of full-length MSP1 as a vaccine candidate against falciparum malaria (EudraCT 2016-002463-33).

opencc-zeroMay 2015View details →

Neutralization Data and Aligned ENV Sequences for Predicting Antibody Affinities using Artificial Neural Networks

Sample file with neutralization data (IC50) for different antibodies and viral strains, adapted from J. Huang, G. Ofek, L. Laub, M. K. Louder, N. A. Doria-Rose, N. S. Longo, H. Imamichi, R. T. Bailer, B. Chakrabarti, S. K. Sharma, S.  M. Alam, T. Wang, Y. Yang, B. Zhang, S. A. Migueles, R. Wyatt, B. F. Haynes, P. D. Kwong, J. R. Mascola, and M. Connors, “Broad and potent neutralization of HIV-1 by a gp41-specific human antibody.,” Nature, vol. 491, no. 7424, pp. 406–12, Nov. 2012.   Aligned ENV sequences downloaded from the HIV Sequence Database (www.hiv.lanl.gov/content/sequence/HIV/mainpage.html). There are 4907 sequences and the alignment length is 1369.

opencc-by-4.0Nov 2023View details →

Antibody panel used for multiplexed antibody-based imaging of Human Pancreas Analysis Program (HPAP) samples by CODEX

This data file details antibodies applied to human pancreas tissue samples from the Human Pancreas Analysis Program (HPAP; RRID:SCR_016202) of the <a href="https://hirnetwork.org/">Human Islet Research Network</a> (HIRN; RRID:SCR_014393). Images will be uploaded for interactive analysis on <a href="https://pancreatlas.org/datasets">Pancreatlas</a> (RRID:SCR_018567) and made available for download via <a href="https://hpap.pmacs.upenn.edu/">PANC-DB</a>. Workflow is documented on protocols.io: <a href="https://dx.doi.org/10.17504/protocols.io.36wgq7dryvk5/v1">dx.doi.org/10.17504/protocols.io.36wgq7dryvk5/v1</a>.Table format adapted from Radtke AJ, Quardokus EM, Saunders DC (2022), <a href="https://doi.org/10.5281/zenodo.7386417">SOP: Construction of Organ Mapping Antibody Panels for Multiplexed Antibody-Based Imaging of Human Tissues</a>. See also: Saunders D; Reihsmann R. <a href="https://doi.org/10.48539/HBM754.BHVR.258">OMAP-13: Organ Mapping Antibody Panel (OMAP) for Multiplexed Antibody-Based Imaging of Human Pancreas with CODEX, v1.0</a>.

opencc-by-4.0Oct 2023View details →

Deep repertoire mining uncovers ultra-broad coronavirus neutralizing antibodies targeting multiple spike epitopes

Abstract: Development of vaccines and therapeutics that are broadly effective against known and emergent coronaviruses is an urgent priority. We screened the circulating B cell repertoires of COVID-19 survivors and vaccinees to isolate over 9,000 SARS-CoV-2-specific monoclonal Abs (mAbs), providing an expansive view of the SARS-CoV-2-specific Ab repertoire. Among the recovered antibodies was TXG-0078, an NTD-specific neutralizing mAb that recognizes diverse alpha- and beta-coronaviruses. TXG-0078 achieves its exceptional binding breadth while utilizing the same VH1-24 variable gene signature and heavy chain-dominant binding pattern seen in other NTD supersite-specific neutralizing Abs with much narrower specificity. We also report the discovery of CC24.2, a pan-sarbecovirus neutralizing antibody that targets a novel RBD epitope and shows similar neutralization potency against all tested SARS-CoV-2 variants, including BQ.1.1 and XBB.1.5. A cocktail of TXG-0078 and CC24.2 protects in vivo, suggesting potential use in variant-resistant therapeutic Ab cocktails and as templates for pan-coronavirus vaccine design.Datasets: This repository contains the 10x Genomic cellranger outputs (matrix and vdj contig files) as well as complied functional characterization dataset used to generate figures on the publication "Deep repertoire mining uncovers ultra-broad coronavirus neutralizing antibodies targeting multiple spike epitopes". Post-vaccination samples for donors CC10, CC25, CC31, CC66 were processed in single 10x Genomic reactions. The timepoints samples consist of multiplexing donors CC10, CC25, CC31, CC66 into one 10x Genomic reaction. Similarly, donors CC26, CC42, CC62, CC67 were multiplexed into a single 10x Genomic reaction.Files:feature names.csv - csv file with sort bait/antigen barcode key feature_reference.csv - csv file with cell hash and antigen barcode referencefiltered_contig_annotations.csv - High-level annotations of each high-confidence contigs from cell-associated barcodes. This is a subset of all_contig_annotations.csv.filtered_contig.fasta - filtered antibody fastafiltered_matrix.mtx.gz - 10x Genomic matrix file for filtered cells. Contains counts data for feature and gene expression library.raw_matrix.mtx.gz - 10x Genomic matrix file for unfiltered cells. Contains counts data for feature and gene expression library.Code: All code used to generate analysis and figures is available under the MIT license on Github

opencc-by-4.0Nov 2023View details →

Dataset for PPP2R5D antibody screening study

This antibody characterization dataset is related to the F1000 research article openly available at F1000Research. This project contains the underlying data included in a study which characterized six commercially-available antibodies for Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform (PPP2R5D). The original study is also available on the Zenodo YCharOS community (<a href="https://doi.org/10.5281/zenodo.10108248">https://doi.org/10.5281/zenodo.10108248</a>).  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).

ABodyBuilder2 predicted structures of paired antibody sequences from Observed Antibody Space.

We used ABodyBuilder2 (https://doi.org/10.1038/s42003-023-04927-7) to model ~1.5M paired antibody structures from paired antibody sequences in Observed Antibody Space (https://opig.stats.ox.ac.uk/webapps/oas/oas_paired/). We have save the structures in folders and sub folders that correspond to the OAS files they came from. Parent folders are named according to study. Within each parent folder are sub folders names according to the files (named by SRA ID) containing sequences. Each structure is then named with the parent file followed by the row number from this file.

opencc-by-4.0Feb 2020View details →

Data from: International multicenter examination of MOG antibody assays.

<div> <div> <div>Raw data set for:</div> </div> Reindl M, Schanda K, Woodhall M, Tea F, Ramanathan S, Sagen J, Fryer JP, Mills J, Teegen B, Mindorf S, Ritter N, Krummrei U, Stöcker W, Eggert J, Flanagan EP, Ramberger M, Hegen H, Rostasy K, Berger T, Leite MI, Palace J, Irani SR, Dale RC, Probst C, Probst M, Brilot F, Pittock SJ, Waters P. <a href="https://www.ncbi.nlm.nih.gov/pubmed/32024795/">International multicenter examination of MOG antibody assays. </a>Neurol Neuroimmunol Neuroinflamm. 2020 Mar 5;7(2). doi: 10.1212/NXI.0000000000000674. Print 2020 Mar 5. PubMed PMID: 32024795; PubMed Central PMCID: PMC7051197. </div> <div> <div>   Objective: To compare the reproducibility of 11 antibody assays for immunoglobulin (Ig) G and IgM myelin oligodendrocyte glycoprotein antibodies (MOG-IgG and MOG-IgM) from 5 international centers. Methods: The following samples were analyzed: MOG-IgG clearly positive sera (n = 39), MOG-IgG low positive sera (n = 39), borderline negative sera (n = 13), clearly negative sera (n = 40), and healthy blood donors (n = 30). As technical controls, 18 replicates (9 MOG-IgG positive and 9 negative) were included. All samples and controls were recoded, aliquoted, and distributed to the 5 testing centers, which performed the following antibody assays: 5 live and 1 fixed immunofluorescence cell-based assays (CBA-IF, 5 MOG-IgG, and 1 MOG-IgM), 3 live flow cytometry cell-based assays (CBA-FACS, all MOG-IgG), and 2 ELISAs (both MOG-IgG). Results: We found excellent agreement (96%) between the live CBAs for MOG-IgG for samples previously identified as clearly positive or negative from 4 different national testing centers. The agreement was lower with fixed CBA-IF (90%), and the ELISA showed no concordance with CBAs for detection of human MOG-IgG. All CBAs showed excellent interassay reproducibility. The agreement of MOG-IgG CBAs for borderline negative (77%) and particularly low positive (33%) samples was less good. Finally, most samples from healthy blood donors (97%) were negative for MOG-IgG in all CBAs. Conclusions: Live MOG-IgG CBAs showed excellent agreement for high positive and negative samples at 3 international testing centers. Low positive samples were more frequently discordant than in a similar comparison of aquaporin-4 antibody assays. Further research is needed to improve international standardization for clinical care.     </div> </div>

Antibody Validation for Cyclical Immunofluorescence Microscopy of Human Kidneys (Part 1, Figures 31 and 33)

This dataset includes Cyclical Immunofluorescnce (CyCIF) images (15-20 channels) of frozen human kidney sections interogated with a panel of 12 validated antibodies designed to evaluate renal tubular cell segmentation (Figures 31 and 32), an a panel of 12 validated antibodies and a lectin designed to evaluate glomerular and glomerulus-associated structures in the normal human kidney (Figure 33). We have attached an excel file (Supplemental Table 2) that includes all of the experimental and (de-identified) patient metadata associated with these images, with information and comments about each of the channel images, the antibodies used, CyCIF cycles, and the cell types and extracellular matrix compartments identified with these combinations of antibodies. Because of the sixze of the images, we have divided this into two separate datasets (Antibody Validation for Cyclical Immunofluorescence Parts 1 and 2).

Antibody Validation for Immunofluorescence Microscopy of Human Kidneys (Part 2, Figures 16-30)

This dataset includes multiplex immunofluorescence images (mostly 3+1 channels) of frozen human kidney sections that have been used to validate a panel of 27 antibodies and 1 lectin designed to define the main cellular and extracellular matrix (ECM) comparments in the normal human kidney. We have attached an excel file (Supplemental Table 1) that includes all of the experimental and (de-identified) patient metadata associated with these images with information, and comments about each of the images, the antibodies used, and the cell types and ECM compoartments identified using these antibodies. Because of the size and number of images used for these studies, we have divided this into two separate datasets (Antibody validation studies Parts 1 and 2).  A subset of these antibodies have also been evaluated for both 2D and 3D cyclical immunofluorescence studies that have been included in separate datasets under this umbrella "community". These are identified in the "Antibodies used" tab in Supplemental Table 1 (CyCIF Cycles).

Antibody Validation for Immunofluorescence Microscopy of Human Kidneys (Part 1, Figures 1-15)

This dataset includes multiplex immunofloresence images (mostly 3+1 channels) of frozen human kidney sections that have been used to validate a panel of 27 antibodies and 1 lectin designed to define the main cellular and extracellular matrix compartments in the normal human kidney. We have attached an excel file (Supplemental Table 1) that includes all of the experimental and (deidentified) patient metadata associated with these images with information and comments about each of the images, the antibodies used, and the cell types and ECM compartments identified using these antibodies. Because of the size and number of images used for these validation studies, we have divided this into two separate datasets (Antibody validation studies Parts 1 and 2).  A subset of these antibodies have also been evaluated for both 2D and 3D cyclical immunofluoresecnce studies that have been included in separate datasets under this umbrella "community". These are identfied in the "Antibodies used" tab in Supplemental Table 1 (CyCIF Cycles).

opencc-zeroMar 2024View details →

Antibodies to Borrelia burgdorferi and Bartonella species in serum and synovial fluid from people with rheumatic diseases

Vector-borne infections may underlie some rheumatic diseases, particularly in people with joint effusions. The aim of this study was to compare serum and synovial fluid antibodies to B. burgdorferi and Bartonella spp. in patients with rheumatic diseases. This observational, cross-sectional study examined paired synovial fluid and serum specimens collected from 110 patients with joint effusion between October 2017 and January 2022. Testing for antibodies to B. burgdorferi (using CDC criteria) and Bartonella spp. via two Indirect Fluorescent Antibody [IFA] assays, was performed as part of routine patient care. There were 30 participants (27%) with positive two-tier B. burgdorferi serology, and 26 participants (24%) with IFA seroreactivity (≥1:256) to B. henselae and/or B. quintana. Both B. burgdorferi IgM and IgG were detected more frequently in synovial fluid than serum: 27% of patients were either IgM or IgG positive in synovial fluid, compared to 15.5% in serum (p = 0.048). Conversely, B. henselae and B. quintana antibodies were detected more frequently in serum than synovial fluid; overall only 2% of patients had positive IFA titers in synovial fluid, compared to 24% who had positive IFA titers in serum (p <0.001). There were no significant associations between B. burgdorferi or Bartonella spp. seroreactivity with any of the clinical rheumatological diagnoses. This study provides preliminary support for the importance of synovial fluid antibody testing for documenting exposure to B. burgdorferi, but not for documenting exposure to Bartonella spp.

opencc-by-4.0Mar 2023View details →

Training and test data for antibody humanness evaluation

### Training and test data for humanness evaluation This data was collected in conjunction with and used for training and testing for Parkinson / Wang et al 2024. The data is organized as follows: - Heavy chain training and multispecies test data (under the heavy chain folder)     - The conslidated cAb rep file contains training human sequences     - The test sample sequences folder contains fasta files with test sequences for each species - Light chain training and multispecies test data (under the light chain folder)     - The conslidated cAb rep file contains training human sequences     - The test sample sequences folder contains fasta files with test sequences for each species - Abybank data (under the abybank compiled data folder)     - This folder contains separate folders for heavy and light chain     - Each subfolder contains test data for a more diverse species set under fasta files for each species - Humanization test data (under the humanization test data folder)     - The sequences in the parental.fa file were originally humanized as part of drug discovery programs     - The experimental.fa file contains the humanization results - IMGT and ADA data (under the imgt test data folder)     - The imgt mab db fa and tsv files contain sequences and species assignments for IMGT mAb DB     - The thera ada fa file contains sequences evaluated in the clinic     - The Therapeutic ADA txt file contains anti drug antibody results for those antibodies - VDJ statistics (under the vdj_statistics_eval folder) The data was retrieved from the following sources. 1. All heavy and light chain training data is from the cAb-Rep database from [Guo et al.](https://pubmed.ncbi.nlm.nih.gov/31649674/) 2. All testing data is from the Observed Antibody Space [(OAS) database](https://opig.stats.ox.ac.uk/webapps/oas/) The training and test data show is after filtering for quality. The testing data was additionally randomly sampled to yield a set of 50,000 sequences for each species, then filtered to remove duplicates. The human test data was checked to ensure no overlap with the human training set. The IMGT, ADA and humanization test data was retrieved from Prihoda et al. and the associated [Github repo](https://github.com/Merck/BioPhi-2021-publication). See Parkinson et al. 2024 and the associated github repos for more details on how models other than SAM / AntPack were evaluated on this data.

opencc-zeroMar 2024View details →

mRNA prime–boost evolves precursors toward VRC01-like broadly neutralizing antibodies in preclinical humanized mouse models

Germline-targeting (GT) protein immunogens to induce VRC01-class broadly neutralizing antibodies (bnAbs) to the CD4 binding site (CD4bs) of the HIV Envelope have shown promise in clinical trials. Here, we preclinically validated the mRNA-LNP delivery of one such immunogen, eOD-GT8, as a soluble self-assembling 60mer nanoparticle in humanized mouse models. In a model with three humanized B cell lineages bearing distinct VRC01-precursor B cell receptors (BCRs) with similar affinities for eOD-GT8, all lineages could be simultaneously primed and undergo diversification and affinity maturation with no sign of exclusionary competition. Boosts drove precursor B cell participation in germinal centers, the accumulation of somatic hypermutations, including in key VRC01-class positions, and affinity maturation to boost and native-like antigens in two of the three precursor lineages. We have preclinically validated a prime-boost regimen of soluble self-assembling nanoparticles delivered by mRNA-LNP, demonstrating that multiple lineages can be primed, boosted, and diversify along the bnAb pathway.

opencc-zeroApr 2024View details →

Transcobalamin receptor antibodies in autoimmune vitamin B12 central deficiency

Vitamin B12 is critical for hematopoiesis and myelination. Deficiency can cause neurologic deficits including loss of coordination and cognitive decline. However, diagnosis relies on vitamin B12 measurement in the blood which may not accurately reflect levels in the brain. Using programmable phage display, we identified an autoantibody targeting the transcobalamin receptor (CD320) in a patient with progressive tremor, ataxia, and scanning speech. Anti-CD320 impaired cellular uptake of cobalamin (B12) in vitro. Despite normal serum levels, B12 was nearly undetectable in her cerebrospinal fluid (CSF). Immunosuppressive treatment and high-dose systemic B12 supplementation were associated with increased CSF B12 levels and clinical improvement. Optofluidic screening enabled rapid isolation of a patient-derived monoclonal antibody that impaired B12 transport across an in vitro model of the blood-brain barrier. Autoantibodies targeting the same epitope of CD320 were identified in 7 other patients with neurologic deficits of unknown etiology, in 6% of healthy controls, and in 21.4% of a neuropsychiatric lupus cohort. In 132 paired serum and CSF samples, detection of anti-CD320 in the blood predicted B12 deficiency in the brain. However, these individuals did not display any hematologic signs of B12 deficiency despite systemic CD320 impairment. Using a genome-wide CRISPR screen, we discovered that the LDL receptor serves as an alternative B12 uptake pathway in hematopoietic cells. These findings dissect the tissue-specificity of B12 transport and elucidate an autoimmune neurologic condition that may be amenable to immunomodulatory treatment and nutritional supplementation.

opencc-zeroApr 2024View details →

PfRH5-induced human monoclonal antibodies show broadly neutralizing activity in P. falciparum clinical isolates

Vaccines to the Plasmodium falciparum reticulocyte binding-like protein homolog 5 (PfRH5) target the blood stage of the parasite's life cycle. PfRH5 has the potential to trigger the production of strain-transcendent antibodies and has proven its efficacy both in pre-clinical and early clinical studies. Vaccine-induced monoclonal antibodies (mAbs) to PfRH5 showed promising outcomes in cultured P. falciparum strains from distinct geographic areas. Here, we assessed the functional impact of vaccine-induced mAbs to PfRH5 on the genetically more complex P. falciparum clinical isolates. We used mAbs isolated from single-cell sorted B-cells of volunteers enrolled in the phase 1a (NCT02181088) clinical trial of the viral-vectored PfRH5 vaccine and used ex-vivo growth inhibition assays (GIA) to assess their efficacy in P. falciparum clinical isolates. Next-generation sequencing (NGS) was used to assess the breadth of genetic diversity in P. falciparum clinical isolates and to infer the genotype/phenotype relationship involved in antibody susceptibility. We showed a dose-dependent inhibition of clinical isolates with three main GIA groups, high, medium, and low. Except for one isolate, our data shows no significant differences in antibody GIA profile between the P. falciparum clinical isolates and the 3D7 reference strain, which harbours the vaccine allele. We observed an additive relationship, where the combination of GIA-low and GIA-medium antibodies resulted in increased GIA activities, having important implications for the contribution of specific monoclonal antibodies in polyclonal IgG responses. While our NGS analysis showed the occurrence of novel mutations in the pfrh5 gene, these mutations were predicted to have little or no functional impact on the antigen's structure or recognition by known mAbs. Our present findings complement earlier reports on the strain transcendent potential of mAbs to PfRH5 and constitute, to our knowledge, the first report on the susceptibility of P. falciparum clinical isolates from natural infections to vaccine-induced mAbs to PfRH5.

opencc-by-4.0Nov 2021View details →

Specifica's recombinant Anti SARS-CoV2 antibodies

These antibodies were selected against the spike protein of SARS-CoV2 from a semi-synthetic antibody library.

opencc-by-4.0Aug 2021View details →

Predominance of antibody-resistant SARS-CoV-2 variants in vaccine breakthrough cases from the San Francisco Bay Area, California

This repository contains the pertinent datasets used in the manuscript, Predominance of antibody-resistant SARS-CoV-2 variants in vaccine breakthrough cases from the San Francisco Bay Area, California.

opencc-by-4.0Dec 2021View details →

Antibody level in Covid Patients

Dataset incude code of patients and level of SARS-CoV-2 IgG antibodies. Antibodies level were mesured with Siemens  ADVIA Centaur®* SARS-CoV-2 IgG (sCOVG).