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15,738 results for “stem cells”
Chicken Embryonic stem cells
<p>Some pictures of chicken embryonic stem cells</p>
Single-nucleus Transcriptomics of IDH1- and TP53-mutant Glioma Stem Cells Displays Diversified Commitment on Highly Invasive Cancer Progenitors
<p><strong>Fig. S1</strong>. <strong>Marker genes for Seurat clusters.</strong> (<strong>A</strong>) distribution of marker genes for cluster 0 on the 2D-UMAP space. (<strong>B</strong>) distribution of marker genes for cluster 1 on the 2D-UMAP space. (<strong>C</strong>) distribution of marker genes for cluster 2 on the 2D-UMAP space. (<strong>D</strong>) distribution of marker genes for cluster 3 on the 2D-UMAP space. (<strong>E</strong>) distribution of marker genes for cluster 4 on the 2D-UMAP space. (<strong>F</strong>) distribution of marker genes for cluster 5 on the 2D-UMAP space. (<strong>G</strong>) Stuck violin plot of marker gene expression for Seurat clusters (bottom panel) and their annotation (right side panel). The violin shape displays the number of the cells expressing a gene, the continuous color panel defines median expression value of a gene from the absence of expression (white) to high expression (dark blue).</p> <p><strong>Fig. S2</strong>. <strong>Expression of genes marking cell malignization.</strong> (<strong>A</strong>) expression of collagens in Surat clusters (bottom panel) (<strong>B</strong>) expression of genes linked to Migration and ECM in Surat clusters (bottom panel) (<strong>C</strong>) expression of genes classified as Proto-oncogenes in Surat clusters (bottom panel). The violin shape displays the number of the cells expressing a gene, the violin color defines the Seurat cluster. Gene expression displayed in log-transformed normalized expression values.</p> <p><strong>Fig. S3</strong>. <strong>Expression of genes involved in proliferation and survival of cancer cells.</strong> (<strong>A</strong>) Genes involved in Wnt-pathway in Surat clusters (bottom panel). (<strong>B</strong>) Genes involved in Akt-pathway in Surat clusters (bottom panel). (<strong>C</strong>) Genes inducing resistance to cancer therapeutics in Surat clusters (bottom panel). The violin shape displays the number of the cells expressing a gene, the violin color defines the Seurat cluster. Gene expression displayed in log-transformed normalized expression values.\</p> <p><strong>Fig. S4</strong>. <strong>Expression of genes marking CSC profile.</strong> (<strong>A</strong>) Ion channel genes in Surat clusters (bottom panel). (<strong>B</strong>) Antioncogenes in Surat clusters (bottom panel). <strong>C</strong>. Stem-cell genes in Surat clusters (bottom panel). (<strong>D</strong>) Antiapoptotic genes in Surat clusters (bottom panel). The violin shape displays the number of the cells expressing a gene, the violin color defines the Seurat cluster. Gene expression displayed in log-transformed normalized expression values.</p> <p><strong>Fig. S5</strong>. <strong>Genes differentially expressed between UMAP clusters</strong>. (<strong>A</strong>) Heatmap for wt-GSCs. (<strong>B</strong>) Heatmap for mt-GSCs. Upper colour panel in the heatmap designates Seurat clusters. Gene expression is indicated by continuous colour panel starting from the most downregulated (blue) to the most upregulated (red).</p> <p><strong>Fig. S6</strong>. <strong>Marker genes defying cell annotations</strong>. (<strong>A</strong>) Stack violin plot displays marker gene expression in wt-GSC clusters. (<strong>B</strong>) Stack violin plot displays marker gene expression in mt-GSC clusters. Genes grouped by cell annotations (side description) and UMAP clusters (down column bar). The violin shape displays the number of the cells expressing a gene, the continuous color panel defines median expression value of a gene from the absence of expression (white) to high expression (dark blue).</p> <p><strong>Fig. S7</strong>. <strong>Differentially expressed proliferation and adhesion pathways comparing mutant samples to wild type.</strong> (<strong>A</strong>) ERBB signalling pathway. (<strong>B</strong>) Wnt signalling pathway. (<strong>C</strong>) Genes linked to Focal adhesion. (<strong>D</strong>) Genes classified as Cell adhesion molecules. Red rectangles display upregulated genes (proteins), green rectangles define downregulated genes (proteins). Pictures obtained by KEGG pathview.</p> <p><strong>Table S1. Glioma genotyping primers</strong></p> <p><strong>Table S2. Smart-seq2 Primers</strong></p>
Culturing Patient-Derived Malignant Hematopoietic Stem Cells in Engineered and Fully Humanized 3D Niches
<p>Data underlying the figures in the publication “Culturing patient-derived malignant hematopoietic stem cells in engineered and fully humanized 3D niches”, published in <em>PNAS,</em><em> <strong>2021</strong>, 118 (40) e2114227118.</em></p> <p><em>DOI: 10.1073/pnas.2114227118</em></p> <p>Table of contents:</p> <p><strong>1. AML data_Gene expression</strong>: qPCR data related to AML samples.</p> <p><strong>2. AML data_Protein</strong>: Luminex data related to AML samples.</p> <p><strong>3. AML data_Supernatant vs Niche</strong>: FACS data comparing AML cells in the supernatant and niche compartments.</p> <p><strong>4. AML data_Supernatant</strong>: FACS data showing AML cells in the supernatant along the time.</p> <p><strong>5. Chemotherapy_2D_FACS</strong>: FACS data showing leukemic cell viability in 2D.</p> <p><strong>6. Chemotherapy_3D_FACS</strong>: FACS data showing leukemic cell viability in 3D (engineered niches).</p> <p><strong>7. MPN data</strong>: FACS data related to MPN samples.</p> <p><strong>8. SV-N_FACS</strong>: FACS data characterizing SV-N.</p> <p><strong>9. SV-N_Gene expression</strong>: qPCR data characterizing SV-N.</p> <p><strong>10. UCSD-AML1_Niche_FACS</strong>: FACS data showing UCSD-AML1 cells in the niche at final analysis.</p> <p><strong>11. UCSD-AML1_Niche_Gene expression</strong>: qPCR data showing UCSD-AML1 cells in the niche at final analysis.</p> <p><strong>12. UCSD-AML1_Supernatant_FACS</strong>: FACS data showing UCSD-AML1 cells in the supernatant along the time.</p> <p><strong>13. UCSD-AML1_Supernatant_Gene expression</strong>: qPCR data related to UCSD-AML1 cells in the supernatant along the time.</p> <p><strong>14. UCSD-AML1_Supernatant_Protein</strong>: Luminex data related to UCSD-AML1 cells in the supernatant along the time.</p> <p><strong>15. Images engineered niches</strong>: Zip archive containing images of engineered niches.</p>
Precancerous liver diseases do not cause increased mutagenesis in liver stem cells
<p>VCF files after variant calling using the HMF pipeline (v4.8) on bam files downloaded from PCAWG as well as from whole genome sequencing of intrahepatic cholangiocyte organoids.</p>
Hypoxia preconditioned mesenchymal stem cells prevent cardiac fibroblast activation and collagen production via leptin
<p><strong>Aims</strong>: Activation of cardiac fibroblasts into myofibroblasts constitutes a key step in cardiac remodeling after myocardial infarction (MI), due to interstitial fibrosis. Mesenchymal stem cells (MSCs) have been shown to improve post-MI remodeling an effect that is enhanced by hypoxia preconditioning (HPC). Leptin has been shown to promote cardiac fibrosis. The expression of leptin is significantly increased in MSCs after HPC, but it is unknown whether leptin contributes to MSC therapy or the fibrosis process. The objective of this study was to determine whether leptin secreted from MSCs modulates cardiac fibrosis.</p> <p><strong>Methods</strong>: Cardiac fibroblast (CF) activation was induced by hypoxia (0.5% O<sub>2</sub>). The effects of MSCs on fibroblast activation were analyzed by co-culturing MSCs with CFs and detecting the expression of a-SMA, SM22a, and collagen IaI in CFs by western blot, immunofluorescence and Sirius red staining. In vivo MSCs antifibrotic effects on left ventricular remodeling were investigated using an acute MI model involving permanent ligation of the left anterior descending coronary artery.</p> <p><strong>Results</strong>: Co-cultured MSCs decreased fibroblast activation and HPC enhanced the effects. Leptin deficit MSCs from Ob/Ob mice did not decrease fibroblast activation. Consistent with this, H-MSCs significantly inhibited cardiac fibrosis after MI and mediated decreased expression of TGF-b/Smad2 and MRTF-A in CFs. These effects were again absent in leptin-deficient MSCs.</p> <p><strong>Conclusion</strong>: Our data demonstrate that activation of cardiac fibroblast was inhibited by MSCs in a manner that was leptin-dependent. The mechanism may involve blocking TGF-b/Smad2 and MRTF-A signal pathway.</p>
Dataset for puplication: Machine Learning in Automated Monitoring of Metabolic Changes Accompanying the Differentiation of Adipose Tissue-Derived Human Mesenchymal Stem cells employing 1H-1H TOCSY NMR
<p>Data set used in the publication: <strong>Machine Learning in Automated Monitoring of Metabolic Changes Accompanying the Differentiation of Adipose Tissue-Derived Human Mesenchymal Stem cells employing <sup>1</sup>H-<sup>1</sup>H TOCSY NMR. </strong></p> <p>Abstract: In this work, the dynamic evolution of adipose tissue-derived human MSCs (AT-derived hMSCs) after fourteen days of cultivation, adiobocytes and osteocytes differentiation has been inspected based on 2D NMR TOCSY using machine learning techniques. Multi-class classification in addition to novelty detection of metabolites was established based on the profile of a control hMSCs sample at four days cultivation and successively detect the absence and the abundance of metabolites in differentiated MSCs following a set of <sup>1</sup>H-<sup>1</sup>H TOCSY profiles. The uploaded files are:</p> <p>File: metabolites_names.xlsx contain the names of the used metabolites.</p> <p>File: metabolites.xlsx</p> <p> column 1: metabolite abbreviation</p> <p>column 2: 2D NMR TOCSY horizontal and vertical frequencies of metabolites in the control group at 4 days cultivation (Ct d4)</p> <p>column 3: 2D NMR TOCSY horizontal and vertical frequencies of metabolites found after 14 days of cultivation (Ct d14)</p> <p>column 4: 2D NMR TOCSY horizontal and vertical frequencies of metabolites found after 14 days of differentiation into adipocytes (AT d14)</p> <p>column 5: 2D NMR TOCSY horizontal and vertical frequencies of metabolites found after14 days of differentiation into osteocytes (OS d14)</p> <p>column 6: 2D NMR TOCSY horizontal and vertical standard frequencies of all metabolites measured at broadband high resolution 600.13 MHz NMR</p>
The supplementary materials of the article"Construction of myocardial patch with mesenchymal stem cells and poly (CL-co-TOSUO)/collagen scaffolds for myocardial infarction repair by coaxial electrospinning"
<p>The supplementary materials of "Construction of myocardial patch with mesenchymal stem cells and poly (CL-co-TOSUO)/collagen scaffolds for myocardial infarction repair by coaxial electrospinning" consist of three figures: Figure S1: The structure and the molecular characteristics of the elastic PCT from gel permeation chromatography; Figure S2: Time series photographs of the rats’ back skin following the subcutaneous transplantation of coaxial electrospun fibrous PCT/collagen scaffolds. Figure S3: Representative histopathological images of the rats' skin following the transplantation of PCT/collagen coaxial nanofibers scaffolds.</p>
ATAC-seq - Definitive endoderm differentiation of human pluripotent stem cells in G1 phase
<p>Backup copy of the processed ATAC-seq data at http://ngs.sanger.ac.uk/production/endoderm/</p>
Interaction of graphene oxide nanoparcticles with human mesenchymal stem cells
<p>Interaction of graphene oxide nanoparcticles with human mesenchymal stem cells visualized by phase-contrast microscopy (Cell-IQ system) over 24 hours. Two concentrations of nanoparticles were used: 5 µg/mL and 25 µg/mL. Four types of particles were used:</p> <table> <tbody> <tr> <td> <p><strong>Notation</strong></p> </td> <td> <p><strong>Diameter (nm)</strong></p> </td> <td> <p><strong>Coating</strong></p> </td> </tr> <tr> <td> <p>P-GOs</p> </td> <td> <p>184 ± 73</p> </td> <td> <p>Linear PEG</p> </td> </tr> <tr> <td> <p>bP-GOs</p> </td> <td> <p>287 ± 52</p> </td> <td> <p>Branched PEG</p> </td> </tr> <tr> <td> <p>P-GOb</p> </td> <td> <p>569 ± 14</p> </td> <td> <p>Linear PEG</p> </td> </tr> <tr> <td> <p>bP-GOb</p> </td> <td> <p>1376 ± 48</p> </td> <td> <p>Branched PEG</p> </td> </tr> </tbody> </table> <p>File names in the archive are as follows:</p> <p>Video S1: Visualization of incubation of cells with P-GOs nanoparticles (5 μg/mL)<br> Video S2: Visualization of incubation of cells with P-GOs nanoparticles (25 μg/mL)<br> Video S3: Visualization of incubation of cells with bP-GOs nanoparticles (5 μg/mL)<br> Video S4: Visualization of incubation of cells with bP-GOs nanoparticles (25 μg/mL)<br> Video S5: Visualization of incubation of cells with P-GOb nanoparticles (5 μg/mL)<br> Video S6: Visualization of incubation of cells with P-GOb nanoparticles (25 μg/mL)<br> Video S7: Visualization of incubation of cells with bP-GOb nanoparticles (5 μg/mL)<br> Video S8: Visualization of incubation of cells with bP-GOb nanoparticles (25 μg/mL)<br> Video S9: Visualization of incubation of cells in the control group (without GO nanoparticles)</p>
Generation of human induced pluripotent stem cells-derived cortical neurons for high throughput imaging of neurite morphology and neuron maturation
<p>Figure 5: Whole cell patch clamping showed the differentiated neurons are functional.</p>
Generation of human induced pluripotent stem cells-derived cortical neurons for high throughput imaging of neurite morphology and neuron maturation
<p>Figure 3 - Neurite outgrowth dataset. Comparing neurite outgrowth at Day1 and 15 post-seeding cortical neural progenitors. </p>
Signalling pathway crosstalk stimulated by L-proline drives mouse embryonic stem cells
<p>Contains data and R code to reproduce paper models, statistics and plots</p>
Fig. 2. 1H– 1H COSY correlations for compounds 6–10 and key HMBC correlations for compounds 1 and 6–10 in Iridoids and bis-iridoids from Valeriana jatamansi and their cytotoxicity against human glioma stem cells
Fig. 2. 1H– 1H COSY correlations for compounds 6–10 and key HMBC correlations for compounds 1 and 6–10.
Assessment of Tolerance of Mobilizing Peripheral Hematopoietic Stem Cells by Plerixafor in Sickle Cell Patients
ClinicalTrials.gov study NCT02212535. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Efficacy of Basiliximab in the Prevention of Acute Graft-versus-host Disease in Unrelated Allogeneic Hematopoietic Stem Cell Transplantation Therapy for Thalassemia Major
ClinicalTrials.gov study NCT02342145. IPD Sharing: Not stated. Countries: 1. Publications: 5.
Mesenchymal Stem Cells Combined With Cord Blood for Treatment of Graft Failure
ClinicalTrials.gov study NCT01763099. IPD Sharing: Not stated. Countries: 1. Publications: 2.
PEPCAD III Substudy: Stem Cell Mobilization
ClinicalTrials.gov study NCT00473499. IPD Sharing: Not stated. Countries: 1. Publications: 6.
Study of the 12-month Efficacy of Stem Cell Injection in Crohn's Disease With Complex Ano-perineal Fistula
ClinicalTrials.gov study NCT05177003. IPD Sharing: Not stated. Countries: 1. Publications: 11.
Study of Mesenchymal Stem Cells for the Treatment of Medically Refractory Ulcerative Colitis (UC)
ClinicalTrials.gov study NCT04543994. IPD Sharing: NO. Countries: 1. Publications: 2.
Efficacy of Bortezomib Consolidation After High-dose Melphalan With Stem Cell Support in Myeloma Patients
ClinicalTrials.gov study NCT00417911. IPD Sharing: Not stated. Countries: 5. Publications: 1.
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.