human pbmcs  (Amgen)

Journal: International Dental Journal

Article Title: Obesity as a Determinant of Periodontal Therapy Outcomes: Insights on Oxidative and Endoplasmic Reticulum Stress Pathways

doi: 10.1016/j.identj.2026.109472

Figure Lengend Snippet: Oxidative stress markers in the study population, stratified by obesity presence, before and after non-surgical periodontal treatment. Total ROS (A and G), cytosolic superoxide (B and H) and mitochondrial superoxide (C and I) in leukocytes, and protein levels of SOD1 (D and J) in PBMCs normalized to the loading control actin with corresponding WB images (E), and serum total antioxidant capacity (F and K). Data are presented as box and whisker plots and were compared using two-factor analysis of variance (ANOVA) followed by post hoc tests. ** P < .01 when comparing baseline vs 12 wk. # P < .05 when comparing groups with vs without obesity. DCFH, diclorodihidrofluoresceína; dHE, dihydroethidium; MitoSOX, Mitochondrial Superoxide Indicator; ns, not significant; PBMCs, peripheral blood mononuclear cells; ROS, reactive oxygen species; SOD1, superoxide dismutase 1.

Article Snippet: Peripheral blood mononuclear cells (PBMCs) comprising monocytes and lymphocytes were isolated from EDTA-collected blood using the MACSprep PBMC Isolation Kit (Miltenyi Biotec, Teterow, Germany), and 5 × 106 cells were used for protein extraction, quantification, and Western blot (WB) analysis.

Techniques: Control, Whisker Assay

Journal: International Dental Journal

Article Title: Obesity as a Determinant of Periodontal Therapy Outcomes: Insights on Oxidative and Endoplasmic Reticulum Stress Pathways

doi: 10.1016/j.identj.2026.109472

Figure Lengend Snippet: Evaluation of UPR markers in PBMCs from study population, stratified by presence of obesity, before and after non-surgical periodontal treatment. Relative protein expression of GRP78 (A and G), ATF6 (B and H), CHOP (C and I), IRE1α (D and J), p-eIF2α (E and K), relative mRNA expression of sXBP1 (F and L) in PBMCs normalized to the loading control actin and representative WB images (M). Data are presented as box and whisker plots and were compared using two-factor analysis of variance (ANOVA) followed by post hoc tests. * P < .05; ** P < .01 when comparing baseline vs 12 wk. ATF6, activating transcription factor 6; BMI, body mass index; CHOP, C/EBP homologous protein; GRP78, Glucose-regulated protein 78; IRE1α, Inositol requiring enzyme 1α; PBMCs, peripheral blood mononuclear cells; p-eIF2α, Phosphorylated eukaryotic translation initiation factor 2 subunit; sXBP1 , spliced Xbox binding protein 1 gene.

Article Snippet: Peripheral blood mononuclear cells (PBMCs) comprising monocytes and lymphocytes were isolated from EDTA-collected blood using the MACSprep PBMC Isolation Kit (Miltenyi Biotec, Teterow, Germany), and 5 × 106 cells were used for protein extraction, quantification, and Western blot (WB) analysis.

Techniques: Expressing, Control, Whisker Assay, Binding Assay

Journal: Bioinformatics

Article Title: Refining sequence-to-expression modelling with chromatin accessibility

doi: 10.1093/bioinformatics/btag199

Figure Lengend Snippet: Highly variable gene expression prediction results. (A) Percent increase in mean Pearson correlation from DNA only to DNA + ATAC for all major cell types in all three multiome datasets, evaluating on highly variable genes versus all genes. (B) Same as a, but showing percent increase in mean Pearson correlation from ATAC only to DNA + ATAC. Solid diagonal lines indicate y = x .

Article Snippet: Multiome human PBMC, single-cell human PBMC with ADTs, multiome human brain, and multiome human jejunum datasets were obtained from www.10xgenomics.com/datasets .

Techniques: Gene Expression

Journal: Bioinformatics

Article Title: Refining sequence-to-expression modelling with chromatin accessibility

doi: 10.1093/bioinformatics/btag199

Figure Lengend Snippet: k -mer attribution and TF-MoDISco motif comparison between the DNA-only and DNA + ATAC models. (A) Change in rank of mean 2-mer importance from the DNA-only to the DNA + ATAC models, across all folds, random seeds, and PBMC (sc) cell types. (B) Jaccard index of the top 10% of 6-mers with positive attribution between the PBMC cell types, with the right triangle showing similarities within the DNA + ATAC models and the left triangle showing similarities within the DNA-only models. (C) TF-MoDISco hits differentially selected in CD14 + monocyte and CD4 T cell models (best Tomtom q -value across CV folds < 0.01), ranked by difference in TF GEx.

Article Snippet: Multiome human PBMC, single-cell human PBMC with ADTs, multiome human brain, and multiome human jejunum datasets were obtained from www.10xgenomics.com/datasets .

Techniques: Comparison

Journal: bioRxiv

Article Title: CHAMPOLLION: Robust Multi-Omics Integration via Inverse Optimal Transport Using Paired Cells

doi: 10.64898/2026.04.28.721317

Figure Lengend Snippet: (a) Schematic representation of the first benchmark experiment. A 10X Multiome dataset is split into a bridge and a test set of pseudo-unpaired cells, with the bridge containing only 3 of the 5 cell types present in the pseudo-unpaired set. (b) LTA (higher is better) and FOSCTTM (lower is better) scores for CHAMPOLLION, MIDAS, and Seurat on the setting described in (a). Bars show the median across n = 5 random initialization seeds, with error bars indicating standard deviation; dots correspond to individual runs. (c) UMAP visualizations of the pseudo-unpaired cells for each method. Cells are colored by modality (left) and by cell type (right). (d) Transport plan inferred by CHAMPOLLION for pseudo-unpaired cells. Rows and columns are ordered by cell type, and the diagonal corresponds to the true pairs between RNA and ATAC profiles. (e) Schematic representation of the second benchmark experiment. For two paired datasets (one Multiome and one CITE-seq), half of the cells are held out as the pseudo-unpaired test set, and increasing fractions of the remainder are used as the bridge to assess the impact of its size on performance. (f) LTA and FOSCTTM scores are reported on both datasets across bridge sizes as described in (e). Lines show median performance across n = 5 seeds, while shaded regions indicate the interquartile range, and points denote individual seed results.

Article Snippet: We retrieved the 10X Multiome Human PBMC (RNA + ATAC) dataset from https://www.10xgenomics.com/datasets/pbmc-from-a-healthy-donor-no-cell-sorting-10-k-1-standard-2-0-0 .

Techniques: Standard Deviation