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.
37
datasets available to search
ShareScore release 0.9.0
Dataset results
37 results for “HLA class I”
HLA Class II specificity assessed by high-density peptide microarray interactions
<p>The ability to predict and/or identify MHC binding peptides is an essential component of T cell epitope discovery; something that ultimately should benefit the development of vaccines and immunotherapies. In particular, MHC class I (MHC-I) prediction tools have matured to a point where accurate selection of optimal peptide epitopes is possible for virtually all MHC-I allotypes; in comparison, current MHC class II (MHC-II) predictors are less mature. Since MHC-II restricted CD4+ T cells control and orchestrate most immune responses, this shortcoming severely hampers the development of effective immunotherapies. The ability to generate large panels of peptides and subsequently large bodies of peptide-MHC-II interaction data is key to the solution of this problem; a solution that also will support the improvement of bioinformatics predictors, which critically relies on the availability of large amounts of accurate, diverse and representative data. Here, we have used recombinant HLA-DRB1*01:01 and HLA-DRB1*03:01 molecules to interrogate high-density peptide arrays, <em>in casu</em> containing 70,000 random peptides in triplicates. We demonstrate that the binding data acquired contains systematic and interpretable information reflecting the specificity of the HLA-DR molecules investigated. Collectively, with a cost per peptide reduced to a few cents combined with the flexibility of recombinant HLA technology, this poses an attractive strategy to generate vast bodies of MHC-II binding data at an unprecedented speed and for the benefit of generating peptide-MHC-II binding data as well as improving MHC-II prediction tools.</p>
Joint host-pathogen genomic analysis identifies hepatitis B virus mutations associated with human NTCP and HLA class I variation
<p>Summary statistics for "Joint host-pathogen genomic analysis identifies hepatitis B virus mutations associated with human NTCP and HLA class I variation" </p><p>Files are organized in the following directory structure:</p><p><strong>G2G/</strong> - Summary statistics of G2G associations (SNPs, HLA, and gene-level analysis). </p><p><strong>HLA/ </strong>- Peptide binding prediction results</p><p><strong>preS1_haplotypes/ - </strong>Resolved intra-host haplotypes of the preS1 binding region. </p><p><strong>DnDs/</strong> - Calculation of intra-host positive selection, within the preS1 binding region. </p><p> </p>
Gene and protein sequence features augment HLA class I ligand predictions
<p>Dataset and analyses supporting the manuscript "Gene and protein sequence features augment HLA class I ligand predictions".</p> <p>The "peptides" files contain the mass-spec detected peptides obtained from HLA ligandomics performed on the indicated tumor lines. </p> <p>The "protein data" files contain the RNAseq data (TPM) and Ribosome profiling data (ribosome occupancy) per protein, for each tumor line. </p> <p>The "source data" zip archive contains the source data underlying the figures of the manuscript.</p> <p>The "HLA ligandome analyses" zip archive contains the R scripts used for all data analysis in the manuscript, including all data and output files. These analyses can also be found at https://github.com/kasbress/HLA_Ligandome_Analyses/</p> <p> </p> <p> </p>
Data for: Endo-lysosomal assembly variations among Human Leukocyte Antigen class I (HLA-I) allotypes
<p>The extreme polymorphisms of HLA-I proteins enable the presentation of diverse peptides to cytotoxic T lymphocytes (CTL). The canonical endoplasmic reticulum (ER) HLA-I assembly pathway enables presentation of cytosolic peptides, but effective intracellular surveillance requires multi-compartmental antigen sampling. Endo-lysosomes are generally sites of HLA class II assembly, but human monocytes and monocyte-derived dendritic cells (moDCs) also contain significant reserves of endo-lysosomal HLA-I molecules. We hypothesized variable influences of HLA-I polymorphisms upon outcomes of endo-lysosomal trafficking, as the stabilities and peptide occupancies of cell surface HLA-I are variable. Consistent with this model, when the endo-lysosomal pH of moDCs is disrupted, HLA-B allotypes display varying propensities for reductions in surface expression, with HLA-B*08:01 or HLA-B*35:01 being among the most resistant or sensitive respectively, among eight tested HLA-B allotypes. Perturbations of moDC endo-lysosomal pH result in redistribution of HLA-B*35:01, but not HLA-B*08:01, to LAMP1+ compartments and increase HLA-B*35:01 peptide receptivity. These findings reveal the intersection of the vacuolar cross-presentation pathway with a constitutive assembly pathway for some HLA-B allotypes. Notably, cross-presentation of epitopes derived from two soluble antigens was also more efficient for B*35:01 compared to B*08:01, even when matched for T cell response sensitivity, and more affected by cathepsin inhibition. Thus, HLA-I polymorphisms dictate the degree of endo-lysosomal assembly, which can supplement ER assembly for constitutive HLA-I expression and increase the efficiency of cross-presentation.</p>
HLA class I Sanger sequences data of Honduras HIV cohort
<p>HLA polymorphisms represent the strongest genetic modifier of HIV disease progression. Diverse HLA distribution can lead to distinct HIV control landscapes at the population level. We aimed to describe HLA allele and haplotype frequencies (linkage disequilibrium, LD), CCR5-Δ32 frequency and the impact of these variants on HIV disease outcome. HLA class I (cI) loci were typed at 4-digit resolution, and CCR5 variants were determined in 402 HIV clade B-infected, ART-naïve individuals from Honduras. HLA LD were assessed using Fisher's exact test. Using univariable and multivariable analyses we evaluated HLA associations with HIV pVL and CD4 counts. We did not find any effect on HIV control between CCR5 genotypes. Previously defined HLA associations were found: <em>B*57:01/03</em>, <em>B*42:01</em>, <em>A*25:01</em> and <em>C*12:03</em> (protective), and <em>B*53:01</em> and <em>A*68:01</em> (risk). Being consistent with our previous research in a Mesoamerican HIV cohort, Amerindian <em>B*35:12</em> was associated to poor HIV control. Other HLA-HIV associations not previously described were <em>C*03:04</em> and <em>B*08:01</em> that were associated with higher pVL. Overall, this first report highlights the immunogenetic uniqueness admixture of the Honduras population that express Amerindian, Caucasian and African HLA subtypes. These findings not only support this cohort as ideal for identifying HLA correlates of HIV control but also may improve future research regarding allotransplantation and disease association.</p>
Data for: Endo-lysosomal assembly variations among Human Leukocyte Antigen class I (HLA-I) allotypes
Open the record for dataset details and reuse information.
HLA Class II specificity assessed by high-density peptide microarray interactions
Open the record for dataset details and reuse information.
HLA class I Sanger sequences data of Honduras HIV cohort
Open the record for dataset details and reuse information.
Amino acid variation in HLA class II proteins is a major determinant of humoral response to common viruses - GWAS summary results
<p>Online Supplementary Dataset of the manuscript "Amino acid variation in HLA class II proteins is a major determinant of humoral response to common viruses": http://www.cell.com/ajhg/fulltext/S0002-9297(15)00372-9</p>
HLA class I and class II allelic profile of healthy Lebanese population
<p class="MsoNormal"><strong><span>Background</span></strong><span>. This study examined the origin of present-day Lebanese using high-resolution HLA class I and class II allele and haplotype distributions. The study subjects comprised 152 unrelated individuals, and their HLA class I and class II alleles and two-locus and five-locus haplotypes were compared with those of neighboring and distant communities </span><span>using genetic distances, neighbor-joining dendrograms, correspondence, and<strong> </strong>haplotype analyses</span><span>. </span><span>HLA class I (<em>A</em>, <em>B</em>, <em>C</em>) and class II (<em>DRB1</em>, <em>DQB1</em>) were genotyped at a high-resolution level by PCR-SSP. </span></p> <p class="MsoNormal"><strong><span>Results</span></strong><span>. In total, 76 alleles across the five HLA loci were detected: <em>A*03:01</em> (17.1%), <em>A*24:02</em> (16.5%), <em>B*</em></span><em><span>35:01</span></em><span> (25.7%), <em>C*</em></span><em><span>04:01</span></em><span> (25.3%), and </span><em><span>C*</span></em><em><span>07:01</span></em><span> (20.7%) were t</span><span>he most frequent class I alleles, while <em>DRB1*</em></span><em><span>11:01</span></em><span> (34.2%) and <em>DQB1*03:01</em> (43.8%) were the most frequent class II alleles. All pairs of HLA loci were in significant linkage disequilibrium. The most frequent two-locus haplotypes recorded were <em>DRB1*11:01</em></span><span>~</span><em><span>DQB1*03:01</span></em><span> (30.9%), <em>B*35:01</em>-<em>C*04:01</em> (20.7%), <em>B*35:01</em></span><span>~</span><em><span>DRB1*11:01</span></em><span> (13.8%), and <em>A*24:02</em></span><span>~</span><em><span>B*35:01</span></em><span> (10.3%). Lebanese appear to be closely related to East Mediterranean communities such as Levantines (Palestinians, Syrians, and Jordanians), Turks, Macedonians, and Albanians. However, Lebanese appear to be distinct from North African, Iberian, and Sub-Saharan communities. </span></p> <p class="MsoNormal"><strong><span>Conclusions</span></strong><span>. Collectively, this indicates a limited genetic contribution of Arabic-speaking populations </span><span>(from North Africa or the Arabian Peninsula</span><span>) and Sub-Saharan communities to the present-day Lebanese gene pool.</span><strong><span> </span></strong><span>This confirms the notion that Lebanese population are of mixed East Mediterranean and Asian origin, with a marked European component.</span></p>
Human Leukocyte Antigen (HLA) Class I Haplotype Mismatched Natural Killer Cell Infusions
ClinicalTrials.gov study NCT00660166. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Association of HY-restricting HLA Class II Alleles, Sex of Firstborn Child, and Pregnancy Outcome in RPL Patients
ClinicalTrials.gov study NCT05342948. IPD Sharing: Not stated. Countries: 1. Publications: 2.
HLA class I and class II allelic profile of healthy Lebanese population
Open the record for dataset details and reuse information.
Data from: A large fraction of HLA class I ligands are proteasome-generated spliced peptides
The proteasome generates the epitopes presented on human leukocyte antigen (HLA) class I molecules that elicit CD8+ T cell responses. Reports of proteasome-generated spliced epitopes exist, but they have been regarded as rare events. Here, however, we show that the proteasome-generated spliced peptide pool accounts for one-third of the entire HLA class I immunopeptidome in terms of diversity and one-fourth in terms of abundance. This pool also represents a unique set of antigens, possessing particular and distinguishing features. We validated this observation using a range of complementary experimental and bioinformatics approaches, as well as multiple cell types. The widespread appearance and abundance of proteasome-catalyzed peptide splicing events has implications for immunobiology and autoimmunity theories and may provide a previously untapped source of epitopes for use in vaccines and cancer immunotherapy.
Data from: A large fraction of HLA class I ligands are proteasome-generated spliced peptides
Open the record for dataset details and reuse information.
Expression levels of HLA-DRB and HLA-DQ are associated with MHC Class II haplotypes in healthy individuals and rheumatoid arthritis patients
GEO Series GSE163605. Homo sapiens. 86 samples. Type: Expression profiling by high throughput sequencing.
HLA Class II analysis of human pancreatic beta cells
GEO Series GSE121863. Homo sapiens. 18 samples. Type: Expression profiling by high throughput sequencing.
Simultaneous identification of DNA variation and methylation at HLA class II locus and immune gene promoters using targeted SureSelect Methyl-Sequencing
GEO Series GSE238121. Homo sapiens. 6 samples. Type: Other; Methylation profiling by high throughput sequencing.
Allelic variation in Class I HLA determines pre-existing memory responses to SARS-CoV-2 that shape the CD8+ T cell repertoire upon viral exposure
GEO Series GSE188429. Homo sapiens. 380 samples. Type: Expression profiling by high throughput sequencing; Other.
γδ T cells are effectors of immunotherapy in cancers with HLA class I defects
GEO Series GSE216534. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing; Other.
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.