Similar Datasets
Project description:We used single cell multiome (ATAC and RNA) sequencing to profile 85266 islet cells from 20 individuals, including islets from non-diabetic, pre-diabetic and type 2 diabetic (T2D) donors. We characterize changes in regulatory programs of islet cell types and subtypes in T2D progression, describe the relationship of these programs to genetic risk for T2D, and use allelic imbalance mapping to define cell type-specific functions for candidate T2D causal variants.
2023-02-07 | GSE200044 | GEO
Project description:Mesenchymal stem cells (MSC) are multipotent stem cells that can differentiate into multiple cell types, including osteoblasts, chondrocytes and adipocytes. Osteoblast differentiation is reduced during osteoporosis development, resulting in reduced bone formation. Further, MSC isolated from different donors possess distinct osteogenic capacity. In this study, we used single-cell mul-tiomic analysis to profile the transcriptome and epigenome of MSC from four healthy donors. Da-ta were obtained from ~1,300 to 1,600 cells for each donor. These cells were clustered into four groups, indicating that MSC from different donors have distinct chromatin accessible regulatory elements for regulating gene expression. To investigate the mechanism by which MSC undergo os-teogenic differentiation, we used the chromatin accessibility data from the single-cell multiome data to identify individual-specific enhancer-promoter pairs and evaluated the expression levels and activities of the transcriptional regulators. The MSC from four donors showed distinct dif-ferentiation potential into osteoblasts. MSC of donor one showed the largest average motif activi-ties, indicating that MSC from donor one was most likely to differentiate into osteoblasts. The re-sults of our validation experiments were consistent with the bioinformatics prediction. We also tested the enrichment of GWAS signals of several musculoskeletal disease traits in the patient-specific chromatin accessible regions identified in the single-cell multiome data, including osteo-porosis, osteopenia, and osteoarthritis. We found that osteoarthritis-associated variants were on-ly enriched in the regions identified from donor four. In contrast, osteoporosis and osteopenia variants were enriched in regions from donor one and least enriched in donor four. Since osteo-porosis and osteopenia are related to the density of bone cells, the enrichment of variants from these traits should be correlated with the osteogenic potential of MSC. In summary, this study provides large-scale data to link regulatory elements with their target genes to study the regula-tory relationships during the differentiation of mesenchymal stem cells and provide a deeper in-sight into the gene regulatory mechanism.
2024-02-16 | GSE255646 | GEO
Project description:Bulk RNAseq was performed across 3 biological donors of MSCs transduced with EcCAR (EcCAR-MSCs) or untransduced (UTD-MSCs)
2024-04-01 | GSE256355 | GEO
Project description:In order to understand the genomic and transcriptomic variability of the axolotl pallium, as well as reconstruct their intrinsic gene regulatory networks, we performed single-nucleus multiome sequencing (RNA and open chromatin) of whole axolotl pallium.
2022-07-20 | E-MTAB-11666 | biostudies-arrayexpress
Project description:Bovine chondrocyte-seeded and mesenchymal stem cell (MSC)-seeded agarose were cultured for 28 days in chemically defined media containing 10 ng/mL TGF-beta3. Chondrogenic differentiated MSCs were compared to chondrocytes at this timepoint and to undifferentiated MSCs harvested at day 0. Donor-matched sets of chondrocytes and MSCs were used, with three donors total.
2010-10-02 | E-GEOD-18394 | biostudies-arrayexpress
Project description:To compare the gene expression profile of hBM-MSCs at early (P3), late-passage (P7), and UBC gene knockdown (KD) from three different donors, we performed one-color microarray-based gene expression analysis.
2016-10-18 | GSE88806 | GEO
Project description:To obtain genetic evidence about the interaction between MSCs and metastatic NB cancer cells in bone marrow (BM), we isolated bone marrow-derived MSCs from children with NB and compared their global expression patterns with MSCs obtained from normal pediatric donors using the Agilent 44K microarrays. A total of eight different donors (four NB patients and four healthy donors) were analyzed and three independent microarrays hybridizations were performed for each donor.
2012-06-30 | E-GEOD-35133 | biostudies-arrayexpress
Project description:Transcriptional profiling of human MSCs comparing control MSCs with parathyroid hormone (PTH)-stimulated MSCs. PTH-stimulated MSCs were treated with 0.1 nM recombinant human PTH (N-terminal fragment, amino acids 1-34) for 48 hours. Human MSCs were isolated from a bone marrow sample obtained from a healthy adult volunteer. Two-condition experiment: control MSCs vs. PTH-stimulated MSCs. 1 control MSCs and 1 PTH-stimulated MSCs.
2014-02-01 | E-GEOD-43148 | biostudies-arrayexpress
Project description:Human mesenchymal stem cells or multipotent stromal cells (MSCs) are of interest for clinical therapy, in part because of their capacity for proliferation and differentiation. However, results from clinical trials and in vitro models have been variable, possibly due to MSC heterogeneity and a lack of standardization between MSC in vitro expansion protocols. Here we defined changes in MSCs during expansion in vitro. In low density cultures, MSCs expand through distinct lag, exponential growth and stationary phases. We assayed cultures of passage 2 human MSCs from three donors at low density (50 cells/cm2) at about 5% confluence on Day 2 and after the cultures had expanded to about 70% confluence on Day 7. On Day 2 genes involved in cell division were up-regulated. On Day 7 genes for cell development were up-regulated. The variations between three donors were less than the variation within the expansion of MSCs from a single donor. The microarray data for selected genes were confirmed by real-time PCR, ELISA and FACScan. About 50% of cells at Day 2 were in S-phase compared to 10% at Day 7. The results demonstrated major differences in early and late stage cultures of MSCs that should be considered in using the cells in experiments and clinical applications. Experiment Overall Design: We assayed cultures of passage 2 human MSCs from three donors at low density (50 cells/cm2) at about 5% confluence on Day 2 and after the cultures had expanded to about 70% confluence on Day 7.
2008-06-16 | E-GEOD-9520 | biostudies-arrayexpress
Project description:We report the application of next-generation sequencing (NGS) to analysis the gene expression profile among three different cells:SF-MSCs, iPSCs and iPSC-MSCs. Our results shown that iPSC-MSCs were more similar to SF-MSCs than iPSCs.
2018-10-04 | GSE120800 | GEO