RNAseq for cultured Control and TgAPPsweOCN BMSCs (sorted Ai9+ Osteoblast-linage cells)
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PROVIDER: PRJNA776261 | ENA |
REPOSITORIES: ENA
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Project description:Purpose: To investigate if and how APPswe in OCN-Cre+ OB-lineage cells gives rise to the brain and behavior phenotypes, we purified OCN-Cre+ BMSCs (marked by tdTomato+, believed to be OB progenitors) from both the 6-MO control (OCN-Cre; Ai9) and TgAPPsweOCN; Ai9 mice using fluorescence-activated cell sorting (FACS) and then subjected them to RNA-seq analysis Methods: (1)the whole bone marrow cells of 6-month-old OCn-Cre;Ai9 andTgAPPswe;OCn-Cre;Ai9 flushed out from long bones of mice with DMEM were filtered through a 70-mm filter mesh, washed, re-suspended, and then plated in 100-mm dishes with growth medium (DMEM plus 10% FBS), which were incubated at 37oC with 5% CO2. The non-adherent cells were removed 72 hours after changing the medium. The attached bone marrow cells were cultured with the growth medium for 7 days. These cells were then resuspended and plated at culture dishes and cultured for another 3-6 days with the same growth medium. These cells, so called BMSCs. (2)Then cell media were removed from culture dishes and cells were rinsed with PBS. Trypsin solution was added to incubate at 37°C for 2 min. The detached adherent cells were centrifuged, and the pellet cells were washed with 1 ml cold PBS, and finally resuspended in 0.5 ml PBS with 1% FBS for flow cytometry analysis. Flow cytometric analysis was performed by use of a flow cytometer in CWRU core facility. Acquisition and analysis were performed by using FACSDiva 8.0.1 software (BD).(3)Total RNAs were extracted from purified Td+ OB-progenitor cells from OCN-Cre; Ai9 and TgAPPsweOCN; Ai9 mice by flow cytometer. RNA Integrity Number (RIN) was accessed for every sample, and the samples were considered qualified with RIN> 2. These RNA samples were then subjected to RNA-seq analyses by BGI America (Cambridge, MA) using the DNBseq platform. Firstly, we removed the reads mapped to rRNA and obtained the raw data with 52.47 Mb reads. After filtering low-quality, adaptor-polluted and high content of unknown base reads in the sequencing reads, 51.9 Mb clean reads were obtained per sample on average. Then clean reads were mapped to reference genome using HISAT2. On average 92.91% reads were mapped and the uniformity of the mapping result for each sample suggests that the samples were comparable. Comparisons to RNAseq were normalized to fpkm Results: 917 up- and 1825 down-regulated genes were identified in APPswe+ OB progenitors. Among these genes, 154 up- and 269 down-regulated genes encode secreted proteins. Interestingly, go analysis showed that most up-regulated genes are involved in inflammatory response, cytokine production, and cytokine/chemokine-mediated signaling pathways; and most down-regulated genes are implicated in cell cycle, cell proliferation, and bone mineralization. Conclusions: Increased cytokines and chemokines in APPswe+ OB-progenitors, indicating that APPswe+ OB progenitors may undergo cellular senescence.
2021-11-30 | GSE186827 | GEO
Project description:We performed microarray analysis to determine the expression profiles of miRNAs during osteoblast differentiation of BMSCs
2019-03-11 | GSE115197 | GEO
Project description:We performed microarray analysis to determine the expression profiles of circRNAs during osteoblast differentiation of BMSCs
2019-03-11 | GSE115196 | GEO
Project description:The cross-talk between mesenchymal stem cells (MSCs) and cancer cells remains controversial. It is imperative to understand how MSC and tumor cells communicate with each other and whether the MSC responds to the tumor according to its stage of progression. We used microarrays to detail the global programme of gene expression in human BMSCs either cultured alone or co-cultured with colon cancer cells HT29 or HCT116 respectively
2017-10-31 | GSE106325 | GEO
Project description:Our preliminary data shows that dietary ACNs increased osteoblast differentiation and function in human osteoblasts, as well as increased osteoblast differentiation and reduced bone resorption in transgenic medaka. In cultured human osteoblasts, ACNs and resveratrol enhanced growth, reduced apoptosis and increased the expression of HDACs and PGC-1, suggesting that ACNs alter epigenetic regulation and mitochondrial biogenesis
2023-08-08 | GSE200683 | GEO
Project description:Our preliminary data shows that dietary ACNs increased osteoblast differentiation and function in human osteoblasts, as well as increased osteoblast differentiation and reduced bone resorption in transgenic medaka. In cultured human osteoblasts, ACNs and resveratrol enhanced growth, reduced apoptosis and increased the expression of HDACs and PGC-1, suggesting that ACNs alter epigenetic regulation and mitochondrial biogenesis
2023-08-08 | GSE200682 | GEO
Project description:We identified microRNA-188 differentially expressed in the BMSCs of aged and young mice and influented on BMSCs differentiation with ageing. Then we used microarrays to detail the osteogenic gene expression during osteogenic differention of BMSCs from 188KO mice.
2014-12-02 | GSE63724 | GEO
Project description:Bone marrow mesenchymal stem cells (BMSCs) differentiate into various mature cell types, including adipocytes and osteoblasts, which is determined by genetic, molecular mediators and local microenvironment. With age, BMSCs become inclined to undergo differentiation into adipocytes rather than osteoblasts, resulting in an increased number of adipocytes and a decreased number of osteoblasts, causing osteoporosis. The dysregulated the gene expression in BMSCs during aging were analyzed. We used microarrays to detail the global programme of gene expression duing aing in BMSCs.
2018-08-15 | GSE116925 | GEO
Project description:Role of FGF23 and DMP1 in osteoblastogenesis in cultured BMSCs at single cell level
| PRJNA1001030 | ENA
Project description:Abstract Background: Bone marrow stromal cells (BMSCs) are being used for immune modulatory, anti-inflammatory and tissue engineering applications, but the properties responsible for these effects are not completely understood. Human BMSCs were characterized to identify factors that might be responsible for their clinical effects and biomarkers for assessing their quality. Methods: Early passage BMSCs prepared from marrow aspirates of 4 healthy subjects were compared to 3 human embryonic stem cell (hESC) samples, CD34+ cells from 3 healthy subjects and 3 fibroblast cell lines. The cells were analyzed with oligonucleotide expression microarrays with more than 35,000 probes. Results: BMSC gene expression signatures of BMSCs differed from those of hematopoietic stem cells (HSCs), hESCs and fibroblasts. Genes up-regulated in BMSCs were involved with cell movement, cell-to-cell signaling and interaction and proliferation. The BMSC up-regulated genes were most likely to belong to integrin signaling, integrin linked kinase (ILK) signaling, NFR2-mediated oxidative stress response, regulation of actin-based motility by Rho, actin cytoskeletal signaling, caveolar-mediated endocytosis, clathrin-mediated endocytosis and Wnt/beta catenin signaling pathways. Among the most highly up-regulated genes were structural extracellular (ECM) proteins: alpha1 and beta1 integrin chains, fibronectin, collagen type IIIalpha1, and collagen type Valpha1 and functional EMC proteins: connective tissue growth factor (CTGF) and transforming growth factor beta induced protein (TGFBI) and ADAM12. Conclusions: Global analysis of human BMSCs suggests that they are mobile, metabolically active, proliferative and interactive cells that make use of integrins and integrin signaling. They produce abundant ECM proteins; some of which may contribute to their clinical immune modulatory and anti-inflammatory effects. Seven samples from early passage BMSCs were prepared from marrow aspirates of healthy subjects and compared to 3 human embryonic stem cell (hESC) samples, CD34+ cells from 3 healthy subjects and 3 fibroblast cell lines. Total RNA from a pool of PBMCs from six healthy subjects was extracted and amplified into aRNA to serve as a reference.
2011-09-20 | E-GEOD-24871 | biostudies-arrayexpress