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15,738 results for “stem cell”
Extraocular muscle stem cells exhibit distinct cellular properties associated with non-muscle molecular signatures
<p>The muscle stem cell (MuSC) population is recognized as functionally heterogeneous. Cranial muscle stem cells, which originate from head mesoderm, can have greater proliferative capacity in culture and higher regenerative potential in transplantation assays when compared to those in the limb. The existence of such functional differences in phenotypic outputs remain unresolved as a comprehensive understanding of the underlying mechanisms is lacking. We addressed this issue using a combination of clonal analysis, live imaging, and scRNA-seq, identifying critical biological features that distinguish extraocular (EOM) and limb (Tibialis anterior, TA) MuSC populations. Time-lapse studies using a MyogenintdTomato reporter showed that the increased proliferation capacity of EOM MuSCs is accompanied by a differentiation delay in vitro. Unexpectedly, in vitro activated EOM MuSCs expressed a large array of distinct extracellular matrix (ECM) components, growth factors, and signaling molecules that are typically associated with mesenchymal non-muscle cells. These unique features are regulated by a specific set of transcription factors that constitute a coregulating module. This transcription factor network, which includes Foxc1 as one of the major players, appears to be hardwired to EOM identity as it is present in quiescent adult MuSCs, in the activated counterparts during growth and retained upon passages in vitro. These findings provide insights into how high-performing MuSCs regulate myogenic commitment by active remodeling of their local environment.</p>
Prediction of mechanistic subtypes of Parkinson's using patient-derived stem cell models
<p>Data and pipelines used to predict mechanistic subtypes of Parkinson's disease using patient-derived stem cell model.</p> <p><strong>Lists of files included;</strong></p> <ul> <li>chemPredPD2022_Imaging process pipelines: pipelines to extract tabular data in Columbus Image Data Storage and Analysis System</li> <li>demo_data_images: a set of data for the Demo</li> <li>ImageData</li> <li>TabularData</li> <li>New test data_PINK1_isoCTRL</li> <li>New test data_SNCA_isoCTRL</li> <li>Tabular_demo_data</li> </ul>
Data supporting 'Small molecule and cell contact-inducible systems for controlling expression and differentiation in stem cells'
<p>Data supporting Soliman et al. 2024. Manuscript describes data collection practices and experimental design.</p>
Rapid and Accurate Identification of Stem Cell Differentiation Stages via SERS and Convolutional Neural Networks
<p><a name="OLE_LINK2"></a><span>Monitoring the transition of cell states during induced pluripotent stem cell (iPSC) differentiation is crucial for clinical medicine and basic research. However, both identification category and prediction accuracy need further improvement. Here, we propose a method combining Surface-Enhanced Raman spectroscopy (SERS) with convolutional neural networks (CNN) to precisely identify and distinguish cell states during stem cell differentiation. First, mitochondria-targeted probes were synthesized by combining AuNRs and mitochondrial localization signal (MLS) peptides to obtain effective and stable SERS spectra signals at various stages of cell differentiation. Then, the SERS spectra served as input datasets, and their distinctive features were learned and distinguished by CNN. As a result, rapid and accurate identification of six different cell states, including the embryoid body (EB) stage, was successfully achieved throughout the stem cell differentiation process with an impressive prediction accuracy of 98.5%. Furthermore, the impact of different spectral feature peaks on the identification results was investigated, which provides a valuable reference for selecting appropriate spectral bands to identify cell states. This is also beneficial for shortening the spectral acquisition region to enhance spectral acquisition speed. These results suggest the potential for SERS-CNN models in quality monitoring of stem cells, advancing the practical applications of stem cells.</span></p>
Supplementary Data for "Epigenetic mechanisms controlling human leukemia stem cells and therapy resistance"
<p><strong>We performed functional genomic profiling of diverse leukemias using label tracing techniques. We identified AML stem cell quiescence is defined by distinct promoter-centered chromatin and gene expression dynamics, and controlled by a novel transcription factor network, which is associated with disease persistence and chemotherapy resistance in multiple patients. </strong></p>
Radiation-Induced Stem Cell Competition and Dose-Rate Effect
<p>A radiation biological effect of a given dose generally decreases with decreasing radiation dose rate, which is known as a “dose-rate effect”. The dose-rate effect demonstrated by many cellular and animal studies. Additionally, recent epidemiological study in high background radiation area in Kerala, India showed that cancer incidence did not increase with increasing cumulative dose (Jayalekshmi et al. Radiat Environ Med 2021). Tissue stem cells have been considered as a target of radiation-induced carcinogenesis. Radiation biological effect could be reduced if damaged stem cells are eliminated by stem cell competition. ICRP described that stem cell competition at the tissue level leaves an ample possibility for a dose-rate effective factor (DREF) value larger than unity, as in the case of the current dose and dose-rate effective factor (DDREF) value (ICRP Publication 131).</p> <p>Cells expressing Lgr5 are one of the major components of intestinal stem cells. Intestinal organoids are three-dimensional cultured tissue model generated from intestinal stem cells. To evaluate a radiation-induced stem cell competition, we established a quantitative method using mixed-organoid derived from two independent fluorescent protein-expressing Lgr5 stem cells, which one of stem cells were irradiated, for mimicking heterogeneous exposure under low-dose-rate irradiation. The organoid-forming potential (OFP) is one of the indices of the abilities of self-renewal, proliferation, and differentiation of stem cells. We found that irradiated stem cells exhibited a growth disadvantage in the mixed organoid, whereas the OFP of irradiated cells per se did not decrease significantly from that of non-irradiated cells.</p> <p>Additionally, we constructed a mathematical model to assess stem cell competition under low-dose-rate irradiation condition. In our model, a stem cell pool, containing a constant number of cells, was assumed, and changed through transition and turnover event. The intact cells turned into damaged cells through transition event which was assumed as the effect of radiation exposure. In the turnover event, a single cell was divided, and a single cell was eliminated from the stem cell pool. The probability of cell division and elimination depended on the properties of cells. The properties of damaged cells were different from that of intact cells. Under very low-dose-rate conditions, the radiation damage was suppressed when the damaged cells were less reproductive and tended to be eliminated compared to the intact cells.</p> <p>These results suggest the radiation-induced stem cell competition can be occurred in the intestine, and the stem-cell competition plays an important role in suppress carcinogenesis under low-dose-rate irradiation condition.</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>
Intermittent ERK oscillations downstream of FGF in mouse embryonic stem cells
<p>Signal transduction networks generate characteristic dynamic activities to process extracellular signals and guide cell fate decisions such as to divide or differentiate. The differentiation of pluripotent cells is controlled by FGF/ERK signaling. However, only a few studies have addressed the dynamic activity of the FGF/ERK signaling network in pluripotent cells at high time resolution. Here, we use live cell sensors in wild-type and Fgf4-mutant mouse embryonic stem cells to measure dynamic ERK activity in single cells, for defined ligand concentrations and differentiation states. These sensors reveal pulses of ERK activity. Pulsing patterns are heterogeneous between individual cells. Consecutive pulse sequences occur more frequently than expected from simple stochastic models. Sequences become more prevalent with higher ligand concentration, but are rarer in more differentiated cells. Our results suggest that FGF/ERK signaling operates in the vicinity of a transition point between oscillatory and non-oscillatory dynamics in embryonic stem cells. The resulting heterogeneous dynamic signaling activities add a new dimension to cellular heterogeneity that may be linked to divergent fate decisions in stem cell cultures.</p>
Supplementary materials of Brain Extract of Subacute Traumatic Brain Injury Promotes Neuronal Differentiation of Human Neural Stem Cells Via Autophagy
<p>Figure S1: Characterization of hNSCs. In proliferate medium, the embryo derived hNSCs could form the neurospheres (A). Markers of NSCs (NES, SOX2, SOX1) were detected (B). The SOX2<sup>+</sup> cells accounted for >95% of all cells (C). Bar scale: 60μm;</p> <p>Figure S2: The proliferation of hNSCs in TBI brain extracts with different phases. Differentiated hNSCs could be labeled with EdU in TBI brain extracts with different phases (A). Ratio of EdU<sup>+</sup> cells was decreased with the progression of days post-injury (B). Bar scale: 75μm; ****: P<0.0001;</p> <p>Figure S3: The GO annotations and KEGG pathway analysis of different expressed pro-teins in acute brain extract and subacute brain extract;</p> <p>Table S1: The protein profiles of brain extract in acute phase and subacute phase after TBI.</p>
Data for PNASnexus article Aldehyde dehydrogenase 3A1 deficiency leads to mitochondrial dysfunction and impacts salivary gland stem cell phenotype
<p>Adult salivary stem/progenitor cells (SSPC) have an intrinsic property to self-renew in order to maintain tissue architecture and homeostasis. Adult salivary glands have been documented to harbor SSPC, which have been shown to play a vital role in the regeneration of the glandular structures post radiation damage. We have previously demonstrated that activation of aldehyde dehydrogenase 3A1 (ALDH3A1) after radiation reduced aldehyde accumulation in SSPC, leading to less apoptosis and improved salivary function. We subsequently found that sustained pharmacological ALDH3A1 activation is critical to enhance regeneration of murine submandibular gland after radiation damage. Further investigation shows that ALDH3A1 function is crucial for SSPC self-renewal and survival even in the absence of radiation stress. Salivary glands from <em>Aldh3a1</em>-null mice have fewer acinar structures than wildtype mice. ALDH3A1 deletion or pharmacological inhibition in SSPC leads to a decrease in mitochondrial DNA copy number, lower expression of mitochondrial specific genes and proteins, structural abnormalities, lower membrane potential, and reduced cellular respiration. Loss or inhibition of ALDH3A1 also elevates ROS levels and accumulation of ALDH3A1 substrate 4-hydroxynonenal (4-HNE, a lipid peroxidation product), leading to decreased survival of murine SSPC that can be rescued by treatment with 4-HNE specific carbonyl scavengers. Our data indicate that ALDH3A1 activity protects mitochondrial function and is important for the regeneration activity of SSPC. This knowledge will help to guide our translational strategy of applying ALDH3A1 activators in the clinic to prevent radiation-related hyposalivation in head and neck cancer patients.</p>
Sequence tracks of Ago2 Neural stem cells and differentiated neurons from single-cells- Related to Fig. 5
<p>Single neural stem cells were isolated from the Hippocampus of newborn mice generated from a hybrid cross. Some of these cells were differentiated In vitro and either the NSC or differentiated neurons were lysed and underwent a reverse transcription. The newly formed cDNA was used as a template to amplify expressed Ago2 transcript which was then sent off for Sanger sequencing. A SNP located within the exon was used to determine whether the transcript from that cell was generated from the maternal or paternal allele.</p>
Bulk NGS/allele quantification - Highly efficient generation of isogenic pluripotent stem cell models using prime editing
<p>This file contains sequencing results for bulk NGS and amplicons covering specific regions of interest related to prime editing of hPSCs. </p>
Highly efficient generation of isogenic pluripotent stem cell models using prime editing - Datasets
<p>This collection contains the following datasets:</p> <p>1. AAVS1 knock-in genotyping</p> <p>2. aCGH karyotyping</p> <p>3. Tabular datasets for associated graphical figures </p> <p> </p>
Common anti-cancer therapies induce somatic mutations in stem cells of healthy tissue
<p>Genome-wide mutation analyses have revealed that specific anti-cancer drugs are highly mutagenic to cancer cells, but the mutational impact of anti-cancer therapies on normal cells is not known. Here, we examine genome-wide somatic mutation patterns in 42 healthy adult stem cells (ASCs) of the colon or the liver from 14 colorectal cancer patients (mean of 3.2 ASC per donor) that received systemic chemotherapy and/or radiotherapy. The platinum-based chemo-drug Oxaliplatin induces on average 535±260 mutations in colon ASC, while 5-FU shows a complete mutagenic absence in most colon ASCs. In contrast with the colon, normal liver ASCs escape mutagenesis from systemic treatment. Radiation results in the accumulation of 50-100 5-10,000bp deletions and structural rearrangements in colon ASCs. Thus, while chemotherapies are highly effective at killing cancer cells, their systemic use also increases the mutational burden of long-lived normal stem cells responsible for tissue renewal thereby increasing the risk for developing second cancers.</p>
Datasets accompanying "Deciphering the heterogeneity of differentiating hPSC-derived corneal limbal stem cells through single-cell RNA-sequencing"
<p>Datasets include two seurat objects: one with all unfiltered cells and raw expression data (seu_unfiltered.rds) and one dataset with normalised expression and latest annotations (differentiation_object_latest.rds). Additionally, a single-cell object containing post-(py)SCENIC analysis is added (ipsc_scenic.h5ad).</p>
April 7, 2024 (v1) Image Open Tuning apicobasal polarity and junctional recycling in the hemogenic endothelium orchestrates the morphodynamic complexity of emerging pre-hematopoietic stem cells —Source data 5 relative to Figure 7 - Figure Supplement 4
<p>Source data file relative to <strong><span>Figure 7 – figure supplement 4 Panel A</span></strong></p> <p><span>Raw image of agarose gel showing the 2 alternative mRNAs encoding for ArhGEF11 in control animals (left track, control) and after injection of the MO at the one cell stage (right track, +MO at 2 and 5ng). The source data includes the raw files (native format .scn and open source format .tiff) as well as a pdf file showing both the full scale image and the cropped image selected for the figure.<br></span></p>
Transcriptomic characterization of 2D and 3D human induced pluripotent stem cell-based in vitro models as New Approach Methodologies for developmental neurotoxicity testing
<p><strong>Abstract:</strong> The safety and developmental neurotoxicity (DNT) potential of chemicals remain critically understudied due to limitations of current in vivo testing guidelines, which are low throughput, resource-intensive, and hindered by species differences that limit their relevance to human health. To address these issues, robust new approach methodologies (NAMs) using deeply characterized cell models are essential. This study presents the comprehensive transcriptomic characterization of two advanced human-induced pluripotent stem cell (hiPSC)-derived models: a 2D adherent and a 3D neurosphere model of human neural progenitor cells (hiNPCs) differentiated up to 21 days. Using high-throughput RNA sequencing, we compared gene expression profiles of 2D and 3D models at three developmental stages (3, 14, and 21 days of differentiation). Both models exhibit maturation towards post-mitotic neurons, with the 3D model maturing faster and showing a higher prevalence of GABAergic neurons, while the 2D model is enriched with glutamatergic neurons. Both models demonstrate broad applicability domains, including excitatory and inhibitory neurons, astrocytes, and key endocrine and especially the understudied cholinergic receptors. Comparison with human fetal brain samples confirms their physiological relevance. This study provides novel in-depth applicability insights into the temporal and dimensional aspects of hiPSC-derived neural models for DNT testing. The complementary use of these two models is highlighted: the 2D model excels in synaptogenesis assessment, while the 3D model is particularly suited for neural network formation as observed as well in previous functional studies with these models. This research marks a significant advancement in developing human-relevant, high-throughput DNT assays for regulatory purposes.</p> <p><strong>This data sets contains:</strong></p> <p><strong>Tab. S1</strong> - Significant genes results</p> <p><strong>Tab. S2</strong> - Enriched pathways_GO_Biological Processes</p> <p><strong>Tab. S3</strong> - Enriched pathways_GO_Cellular Components</p> <p><strong>Tab. S4</strong> - Enriched pathways_GO_Molecular Function</p> <p><strong>Tab. S5</strong> - Enriched pathways_KEGG</p> <p><strong>Tab. S6</strong> - EnrichEnriched pathways_Panther</p> <p><strong>Tab. S7</strong> - Enriched pathways_Reactome</p> <p><strong>Tab. S8</strong> - Gene counts</p> <p><strong>Tab. S9</strong> - Gene selection for targeted analysis</p>
Data files for "Mitochondria-enriched protrusions are associated with brain and intestinal stem cells in Drosophila"
<p>This entry is for our report "Mitochondria-enriched protrusions are associated with brain and intestinal stem cells in <em>Drosophila" </em>by Sharyn A. Endow, Sara E. Miller & Phuong Thao Ly in <em>Commun Biol </em><strong>2</strong>, 427 (2019). <a href="https://doi.org/10.1038/s42003-019-0671-4">https://doi.org/10.1038/s42003-019-0671-4</a></p> <p>The deposited datasets contain the 1) EM raw images, 2) immunofluorescence microscopy (IFM) raw images, 3) live imaging raw sequences, and 4) data analysis files.</p>
Data from: Drosophila medulla neuroblast termination via apoptosis, differentiation and gliogenic switch is scheduled by the depletion of the neuroepithelial stem cell pool
<p>The brain is consisted of diverse neurons arising from a limited number of neural stem cells. <em>Drosophila</em> neural stem cells called neuroblasts (NBs) produces specific neural lineages of various lineage sizes depending on their location in the brain. In the <em>Drosophila</em> visual processing centre - the optic lobes (OLs), medulla NBs derived from the neuroepithelium (NE) give rise to neurons and glia cells of the medulla cortex. The timing and the mechanisms responsible for the cessation of medulla NBs are so far not known. In this study, we show that the termination of medulla NBs during early pupal development is determined by the exhaustion of the NE stem cell pool. Hence, altering NE-NB transition during larval neurogenesis disrupts the timely termination of medulla NBs. Medulla NBs terminate neurogenesis via a combination of apoptosis, terminal symmetric division via Prospero, and a switch to gliogenesis via Glial Cell Missing (Gcm), however, these processes occur independently of each other. We also show that temporal progression of the medulla NBs is mostly not required for their termination. As the <em>Drosophila</em> OL shares a similar mode of division with mammalian neurogenesis, understanding when and how these progenitors cease proliferation during development can have important implications for mammalian brain size determination and regulation of its overall function.</p>
Data from: Aged-vascular niche hinders osteogenesis of mesenchymal stem cells through paracrine repression of Wnt-axis
<p>Raw data set for: Fleischhacker V, Milosic F, Bricelj M, Kührer K, Wahl-Figlash K, Heimel P, Diendorfer A, Nardini E, Fischer I, Stangl H, Pietschmann P, Hackl M, Foisner R, Grillari J, Hengstschläger M, and Osmanagic-Myers S. Aged-vascular niche hinders osteogenesis of mesenchymal stem cells through paracrine repression of Wnt-axis. Aging Cell. 2024 Jun;23(6):e14139. doi: 10.1111/acel.14139. Epub 2024 Apr 5.</p> <p><span>Age-induced decline in osteogenic potential of bone marrow mesenchymal stem cells (BMSCs) potentiates osteoporosis and increases risk for bone fractures. Despite e</span><span>pidemiology studies reporting concurrent development of vascular- and bone diseases in the elderly, the underlying mechanisms for the vascular-bone cross-talk in aging are largely unknown. </span><span>In this study, we show that accelerated endothelial aging deteriorates bone tissue through paracrine repression of Wnt-driven-axis in BMSCs. <span>Here, we utilize </span>physiologically aged mice<span> in conjunction with our transgenic endothelial progeria mouse model </span>(Hutchinson-Gilford progeria syndrome; HGPS) that<span> displays hallmarks of an aged bone marrow vascular niche</span>. We find bone defects associated with diminished BMSC osteogenic differentiation that implicate the existence of angiocrine factors with long-term inhibitory effects. microRNA-transcriptomics of HGPS-patient plasma combined with aged-vascular niche analyses in progeria mice reveal abundant secretion of Wnt-repressive microRNA-31-5p. Moreover, we show that inhibition of microRNA-31-5p as well as selective Wnt-activator CHIR99021 boost the osteogenic potential of BMSCs through de-repression and activation of the Wnt-signalling, respectively. Our results demonstrate that the vascular niche significantly contributes to osteogenesis defects in aging and pave ground for microRNA-based therapies of bone loss in elderly.</span></p> <h1> </h1>
ScienceDex guides
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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.