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423 results for “Human blood cells”
Antigen-specific CD4+ T cells exhibit distinct transcriptional phenotypes in the lymph node and blood following vaccination in humans
<p><strong>Abstract: </strong><br>SARS-CoV-2 infection and mRNA vaccination induce robust CD4+ T cell responses that are critical for the development of protective immunity. Here, we evaluated spike-specific CD4+ T cells in the blood and draining lymph node (dLN) of human subjects following BNT162b2 mRNA vaccination using single-cell transcriptomics. We analyze multiple spike-specific CD4+ T cell clonotypes, including novel clonotypes we define here using Trex, a new deep learning-based reverse epitope mapping method integrating single-cell T cell receptor (TCR) sequencing and transcriptomics to predict antigen-specificity. Human dLN spike-specific T follicular helper cells (TFH) exhibited distinct phenotypes, including germinal center (GC)-TFH and IL-10+ TFH, that varied over time during the GC response. Paired TCR clonotype analysis revealed tissue-specific segregation of circulating and dLN clonotypes, despite numerous spike-specific clonotypes in each compartment. Analysis of a separate SARS-CoV-2 infection cohort revealed circulating spike-specific CD4+ T cell profiles distinct from those found following BNT162b2 vaccination. Our findings provide an atlas of human antigen-specific CD4+ T cell transcriptional phenotypes in the dLN and blood following vaccination or infection.</p> <p><strong>More Information:</strong></p> <ul> <li><strong>Preprint:</strong> <a href="https://www.researchsquare.com/article/rs-3304466/v1">Research Square.</a></li> <li><strong>Sample information</strong>: data_inventory.csv file.</li> <li><strong>Code</strong> code_github_repo.zip or at the <a href="https://github.com/ncborcherding/COVID_TCR">original github repo</a></li> <li><strong>Interactive Portal</strong>: <a href="https://cellpilot.emed.wustl.edu/">CellPilot</a></li> </ul>
Backpain exercise therapy remodels human epigenetic profiles in buccal and human peripheral blood mononuclear cells: An exploratory study in young male participants
<pre><strong>###### Files description #####</strong><br> <strong>Notes</strong>. 1) "BT" refers to before therapy and "AT" to after therapy. 2) 0 refers to FALSE and 1 to TRUE for binary variables. The provided files have tab-separated columns except the .RDS which is and R output of the mixOmics DIABLO integration analysis. <strong># Questionnaire</strong> > participants_categories.tsv: per participant (rows), output of the clustering with the participant ("ID") category ("category") per class<br> ("class") > questionnaire_agility_metrics.tsv: questionnaire and agility metrics per participant (rows) for the participants ("ID") with at least one paired AT+BT data in one type of biological sample (indicated in the columns "swab", "PBMC", and "plasma") <strong># PTMs</strong> Samples´ names are encoded as PBMC_AT_8_batch1, i.e. cells origin_time upon therapy_ID_batch (we removed _batch column suffix for the <br>processed files). NA indicates an undetected intensity. > raw_PBMC_light_labelled_intensities.tsv: raw intensity of light/endogenous peptides (row) by precursor per sample (column) from PBMC > raw_swab_light_labelled_intensities.tsv: idem from buccal cells > raw_PBMC_heavy_labelled_intensities.tsv: raw intensity of light/endogenous peptides (row) by precursor per sample (column) from PBMC > raw_swab_heavy_labelled_intensities.tsv: idem from buccal cells > raw_PBMC_heavynormalized_intensities.tsv: raw intensity of light peptides normalized by heavy peptides intensity (row) by precursor per <br>sample (column) > raw_swab_heavynormalized_labelled_intensities.tsv: idem from buccal cells > processed_cleaned_PBMC_log2intensities.tsv: processed (heavy normalized, imputed, batch-corrected) intensity of peptides aggregated by modification (PTM, row) by precursor per sample (column) after log2-transformation. The relative abundances are computed from this file. Rows without me/ac suffix represents the amount of unmodified peptide for the considered site. > processed_cleaned_swab_log2intensities.tsv: idem from buccal cells > rel_abundance_PTM_PBMC.tsv: relative abundance computed per precursor, e.g. for a given sample, the H3_K4+H3_K4me1+H3_K4me2+H3_K4me3 <br>relative abundance values must sum to 100, with the relative abundance of H3_K4 representing the absence of modified K4. > rel_abundance_PTM_swab.tsv: idem from buccal cells > tests_from_rel_abundance_PTM_swab_PBMC.tsv: per type of samples ("Sample.origin", i.e.swab of PBMC) and per PTM (rows, "PTM"), report <br>the output of classic (p-values, adjusted with Benjamini-Hochberg (BH), or Benjamini-Yekutieli procedure (BY), from raw and arcsin square <br>root transformed percentage) and PLS-DA tests (VIP - Variable Importance score - and its 95% confidence interval). The percentage of change<br>of each PTM after therapy relative tobefore therapy is reported in "perc_change.AT.over.BT" column. The "is_candidate" indicates if the PTM has been considered as a hit in the swab or PBMC. <strong># Plasma</strong> Samples´ names are encoded as PLASMA_AT_8_batch1, i.e. cells origin_time upon therapy_ID_batch. NA indicates an undetected intensity. > raw_plasma_maxquant_log2ibaq_intensities.tsv: raw data from protein group MaxQuant file. The iBAQ columns are used in later steps. > processed_cleaned_plasma_log2intensities.tsv: processed (imputed, batch-corrected) intensity of protein groups after log2-transformation. > tests_from_intens_plasma.tsv: per protein group ("Proteins.ID"), report the output of classic (p-values, adjusted Benjamini-Hochberg (BH),<br>or Benjamini-Yekutieli procedure (BY), from log2-transformed intensities) and PLS-DA tests (VIP and its 95% confidence interval). The log2 <br>fold change after therapy relative to before therapy is reported in "log2FC.AT.over.BT" column. The "is_candidate" indicates if the protein group has been considered as a hit. <strong># Integration</strong> > circos_input: output of DIABLO analysis with correlation threshold set to 0.7. Use the readRDS R function to open.</pre> <p> </p>
Immune repertoire profiling reveals that clonally expanded B and T cells infiltrating diseased human kidneys can also be tracked in the blood
<p>Recent advances in high-throughput sequencing allow for the competitive analysis of the human B and T cell immune repertoire. In this study we compared Immunoglobulin and T cell receptor repertoires of lymphocytes found in kidney and blood samples of 10 patients with various renal diseases based on next-generation sequencing data.</p>
Engineering of Fully Humanized and Vascularized 3D Bone Marrow Niches Sustaining Undifferentiated Human Cord Blood Hematopoietic Stem and Progenitor Cells
<p>Data underlying the figures in the publication “Engineering of fully humanized and vascularized 3D bone marrow niches sustaining undifferentiated human cord blood hematopoietic stem and progenitor cells”, published in <em>J Tissue Eng., </em><strong>2021</strong>, 12, 2041731421044855.</p> <p>DOI:10.1177/20417314211044855</p> <p> </p> <p>Table of Contents:</p> <p><strong>1. P12-03_TP01_Suppernatant</strong>: Enzyme-linked immunosorbent assay of VEGF concentration in vascularized and not vascularized BM niches.</p> <p><strong>2. P12_WholeNiche</strong>: qPCR data of vascular and osteogenic markers in vascularized and not vascularized BM niches.</p> <p><strong>3. FACs-Overview-SN_relativ</strong>: FACS data showing haematopoietic cell populations in the supernatant after HSC cocoulture in vascularized and not vascularized BM niches.</p> <p><strong>4. FACs-Overview-niche_Relativ</strong>: FACS data showing haematopoietic cell populations in the niche after HSC cocoulture in vascularized and not vascularized BM niches.</p> <p><strong>5. CFU</strong>: Colony formation statistics after HSC cocoulture from vascularized and not vascularized BM niches.</p> <p><strong>6. Cell cycle</strong>: Cell cycle statistics of HSPCs after HSC cocoulture from vascularized and not vascularized BM niches.</p> <p><strong>7. P12_03_AfterHSPC-vs-BeforeHSPCs</strong>: qPCR data of vascular and osteogenic markers in vascularized and not vascularized BM niches after and before HSC cocoulture.</p> <p><strong>8. Scheme</strong>: Vector graphic of experimental setup.</p> <p><strong>9. Images engineered niches</strong>: Folder containing images of engineered niches.</p>
Human dermal microvascular arterial and venous blood endothelial cells and their use in bioengineered dermo-epidermal skin substitutes in vitro and in vivo
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Human dermal microvascular arterial and venous blood endothelial cells and their use in bioengineered dermo-epidermal skin substitutes in vitro and in vivo
<p>The bio-engineering of vascular networks is pivotal to create complex tissues and</p> <p>organs in vitro for regenerative medicine applications. The vascular plexus is needed for a</p> <p>sufficient and fast blood supply after transplantation, and, thus, required for the survival and</p> <p>function of the engineered tissue or organ. Hence, human endothelial cells are an attractive</p> <p>source for bio-engineering purposes, for example human dermal microvascular endothelial</p> <p>cells (HDMECs).</p> <p>So far, a discrimination between arterial and venous blood endothelial cells after</p> <p>isolation of HDMECs from skin biopsies and if arterial and/or venous capillaries are formed in</p> <p>pre-vascularized bio-engineered substitutes was not investigated.</p> <p>In this study, we investigated employedby single cell sequencing for to</p> <p>investigate/compare human arterial and venous endothelial cell markers in human fetal and</p> <p>juvenile skin. Further, we analyzed if these markers are present after isolation of human skin</p> <p>derived endothelial cells under 2D culture conditions. In additionFinally, we investigated</p> <p>assessed if human endothelial cells form distinct arterial and venous capillaries in 3D</p> <p>collagen type I hydrogels, and if these capillaries retain their identity after transplantation.</p> <p>We determinedOur results showed that arterial and venous endothelial cell markers</p> <p>such as NRP1 and NR2F2 are expressed both in fetal and juvenile skin, and are retained after</p> <p>isolation in culture. We could show demonstrate that arterial and venous endothelial cells</p> <p>maintain their differentiation status and form arterial and venous capillaries in 3D in vitro</p> <p>culture systems and that the capillaries inosculate after transplantation.</p> <p>In summary, we could show that we could bio-engineer human arterial, venous, and</p> <p>lymphatic capillaries in a human skin substitute in view of regenerative medicine approaches</p> <p>for clinical applications.</p>
Recombinant Human Thrombopoietin for Mobilization of Peripheral Blood Progenitor Cells for Autologous Transplantation
ClinicalTrials.gov study NCT03014102. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Treatment of SCID Due to ADA Deficiency With Autologous Transplantation of Cord Blood or Hematopoietic CD 34+ Cells After Addition of a Normal Human ADA cDNA by the EFS-ADA Lentiviral Vector
ClinicalTrials.gov study NCT02022696. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Human Menstrual Blood-derived Mesenchymal Stem Cells for Patients With Liver Cirrhosis
ClinicalTrials.gov study NCT01483248. IPD Sharing: Not stated. Countries: 1. Publications: 5.
Studies of the Pathogenesis of HIV Infection in Human Peripheral Blood Cells and/or Body Fluids in People Living With and Without HIV
ClinicalTrials.gov study NCT00001281. IPD Sharing: YES. Countries: 1. Publications: 3.
Examination of B Cell Responses in Human Blood
ClinicalTrials.gov study NCT00806845. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Data from: PCR-Free enrichment of mitochondrial DNA from human blood and cell lines for high quality next-generation DNA sequencing
Recent advances in sequencing technology allow for accurate detection of mitochondrial sequence variants, even those in low abundance at heteroplasmic sites. Considerable sequencing cost savings can be achieved by enriching samples for mitochondrial (relative to nuclear) DNA. Reduction in nuclear DNA (nDNA) content can also help to avoid false positive variants resulting from nuclear mitochondrial sequences (numts). We isolate intact mitochondrial organelles from both human cell lines and blood components using two separate methods: a magnetic bead binding protocol and differential centrifugation. DNA is extracted and further enriched for mitochondrial DNA (mtDNA) by an enzyme digest. Only 1 ng of the purified DNA is necessary for library preparation and next generation sequence (NGS) analysis. Enrichment methods are assessed and compared using mtDNA (versus nDNA) content as a metric, measured by using real-time quantitative PCR and NGS read analysis. Among the various strategies examined, the optimal is differential centrifugation isolation followed by exonuclease digest. This strategy yields >35% mtDNA reads in blood and cell lines, which corresponds to hundreds-fold enrichment over baseline. The strategy also avoids false variant calls that, as we show, can be induced by the long-range PCR approaches that are the current standard in enrichment procedures. This optimization procedure allows mtDNA enrichment for efficient and accurate massively parallel sequencing, enabling NGS from samples with small amounts of starting material. This will decrease costs by increasing the number of samples that may be multiplexed, ultimately facilitating efforts to better understand mitochondria-related diseases.
Targeted gene expression profiling of human myeloid cells from blood and lung compartments of patients with Tuberculosis and other lung diseases
<p>This dataset comprises expression profiles of 43 genes related to MSDC functioning and 5 reference genes in 8 blood samples and 8 brochio-alveolar lavage fluid (BALF) samples from TB patients. Also included are results from blood and BALF of 2 'other lung disease' patients each.</p>
Administering Peripheral Blood Lymphocytes Transduced With a Murine T-Cell Receptor Recognizing Human Thyroglobulin to People With Thyroglobulin Expressing Thyroid Cancer
ClinicalTrials.gov study NCT02390739. IPD Sharing: Not stated. Countries: 0. Publications: 3.
Study for Safety and Efficiency of Therapeutic Angiogenesis for Patients With Limb Ischemia by Transplantation of Human Cord Blood Mononuclear Cell
ClinicalTrials.gov study NCT00518934. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Red Blood Cell ATP Release and Vascular Function in Humans
ClinicalTrials.gov study NCT03404843. IPD Sharing: NO. Countries: 1. Publications: 0.
Treatment of Osteoarthritic Knee With High Tibial Osteotomy and Implantation of Allogenic Human Umbilical Cord Blood-derived Stem Cells.
ClinicalTrials.gov study NCT04234412. IPD Sharing: UNDECIDED. Countries: 0. Publications: 1.
Human Cord Blood Mononuclear Cells in the Treatment of Refractory Diabetic Foot
ClinicalTrials.gov study NCT05999656. IPD Sharing: NO. Countries: 1. Publications: 0.
Data from: PCR-Free enrichment of mitochondrial DNA from human blood and cell lines for high quality next-generation DNA sequencing
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Data from: Human blood and mucosal regulatory T cells express activation markers and inhibitory receptors in inflammatory bowel disease
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International Brain Laboratory public data
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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.