Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA155481 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:This SuperSeries is composed of the following subset Series: GSE27900: Gene expression analysis of mesenchymal stem cells (MSC), osteoblasts and the U2OS (osteosarcoma) cell line GSE35573: ChIP-seq analysis of H3K4Me3- and H3K27Me3-marked chromatin in mesenchymal stem cells (MSCs), osteoblasts derived from MSCs and the osteosarcoma cell line U2OS Refer to individual Series
2012-03-02 | E-GEOD-35576 | biostudies-arrayexpress
Project description:Transcriptional profiling of MSC, Osteoblasts and U2OS cells. The aim was to quantitate relative gene expression in MSC, osteoblasts and U2OS. MSC and osteoblasts were used as normal cells in this study because osteosarcoma most likely originates from MSC or osteoblasts.
2012-03-02 | GSE27900 | GEO
Project description:To determine whether enhanced self-renewal and tumorigenicity in UT2 cells (derived from the second humanM-bM-^@M-^Smouse xenotransplantation of U2OS cell-formed osteosarcoma tissues) correlate with increased expression of stem/progenitor cell-associated genes, we measured global gene expression in MSC, U2OS and UT2 cells by microarray analysis. Compared to U2OS and MSC, molecules involved in regulation of self-renewal signaling pathways of cancer stem cells were also up-regulated in UT2 cells, including those in the Notch, Wnt, and TGF-beta pathways. These data suggest a genetic basis for the enhanced self-renewal and tumorigenicity of osteosarcoma-initiating cell in UT2 cells. MSC, U2OS and UT2 cells were selected for RNA extraction and hybridization on Affymetrix microarrays. We sought to analysis stem/progenitor cell-associated genes and molecules involved in regulation of self-renewal signaling pathways of cancer stem cells between UT2 cells and its parent cells: U2OS (MSC works as positive control here).
2012-12-30 | E-GEOD-30807 | biostudies-arrayexpress
Project description:To determine whether enhanced self-renewal and tumorigenicity in UT2 cells (derived from the second human–mouse xenotransplantation of U2OS cell-formed osteosarcoma tissues) correlate with increased expression of stem/progenitor cell-associated genes, we measured global gene expression in MSC, U2OS and UT2 cells by microarray analysis. Compared to U2OS and MSC, molecules involved in regulation of self-renewal signaling pathways of cancer stem cells were also up-regulated in UT2 cells, including those in the Notch, Wnt, and TGF-beta pathways. These data suggest a genetic basis for the enhanced self-renewal and tumorigenicity of osteosarcoma-initiating cell in UT2 cells.
2012-12-30 | GSE30807 | GEO
Project description:We performed genome-wide gene expression data of high-grade osteosarcoma cell lines, as well as on mesenchymal stem cells, and osteoblasts, and performed global test analysis in order to determine the most significantly affected KEGG pathways. Genome-wide gene expression analysis was performed on 19 high-grade osteosarcoma cell lines. Significantly differentially expressed genes were determined between osteosarcoma cells and two different sets of control samples - osteoblasts [n=3, GEO accession number GSE33382] and mesenchymal stem cells [n=12, GEO accession number GSE28974]. Global test was applied to the different analyses, in order to determine the most affected signaling pathways in osteosarcoma cells.
2013-06-06 | E-GEOD-42351 | biostudies-arrayexpress
Project description:Transcriptional profiling of MSC, Osteoblasts and U2OS cells. The aim was to quantitate relative gene expression in MSC, osteoblasts and U2OS. MSC and osteoblasts were used as normal cells in this study because osteosarcoma most likely originates from MSC or osteoblasts. Cell culture and treatment: U2OS cells were cultured in McCoys 5A media (Invitrogen) containing 10% FBS. MSC and osteoblasts were cultured as described by Jaiswal et al. (J Cell Biochem 64, 295-312; 1997). Cells were treated with 5 uM 5-Azadeoxycytidine (5-Aza-CdR) or 300 nM Trischostatin-A (TSA) for 96 hours or 18 hours, respectively. Microarray analysis: Total RNA was extracted using the Qiagen kit according to the manufacturer's instructions, including a DNase step. RNA was quantified using the NanoDrop ND-100, followed by quality assessment with the 2100 Bioanalyzer (Agilent Technologies). RNA concentrations for individual samples were greater than 200ng/ul, with 28s/18s ratios greater than 2.2 and RNA integrity numbers of 10 (highest). Sample amplification and labeling procedures were carried out using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies) according to the manufacturer's instructions. The labeled cRNA was purified using the RNeasy mini kit (Qiagen) and quantified. RNA spike-in controls (Agilent Technologies) were added to the RNA samples before amplification. 0.75 microgram of samples labeled with Cy3 or Cy5 were mixed with control targets (Agilent Technologies), assembled on Oligo Microarray, hybridized, and processed according to the Agilent microarray protocol. Scanning was performed with the Agilent Scanner G2505B under the default settings recommended by Agilent Technologies. Data analysis: All arrays were subject to the quality checks recommended by the manufacturer. Images were visually inspected for artifacts, and distributions of signal and background intensity of both red and green channels were examined to identify anomalous arrays. No irregularities were observed, and all arrays were retained and used. All calculations were performed using the R statistical computing platform and packages from the Bioconductor bioinformatics software project. To determine the expression levels of genes in MSC, Osteoblasts and U2OS, the data were LOWESS-normalized, the probe intensities of the mock channel (no drug treatment) were extracted and set to the same scale by quantile normalization. Mean of replicate samples were calculated for each probe.
2012-03-02 | E-GEOD-27900 | biostudies-arrayexpress
Project description:Gene expression and ChIP-seq analyses of mesenchymal stem cells, osteoblasts and the U2OS osteosarcoma cell line
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Project description:Osteoblasts are a key component of the endosteal hematopoietic stem cell (HSC) niche and have long been recognized with strong hematopoietic supporting activity. Osteoblast conditioned media (OCM) enhances the growth of hematopoietic progenitors in culture and modulate their engraftment activity. We aimed to characterize the hematopoietic supporting activity of OCM by comparing the secretome of immature osteoblasts to that of their precursor, mesenchymal stromal cells (MSC). Over 300 secreted proteins were quantified by mass spectroscopy in media conditioned with MSC or osteoblasts, with 47 being differentially expressed.
2021-11-15 | MSV000088384 | MassIVE
Project description:Patient-derived bone tumor (osteosarcoma and giant cell tumor of bone) cells, and the normal mesenchymal stem cells and osteoblasts were cultured and subjected to UV crosslinking (UV) at 254 nm or without crosslinking (noUV) as negative controls. Subsequently, RNA-binding proteins (RBPs) were identified by eRIC.
2024-02-28 | PXD038185 | Pride
Project description:Osteoblasts are a key component of the endosteal hematopoietic stem cell (HSC) niche and have long been recognized with strong hematopoietic supporting activity. Osteoblast conditioned media (OCM) enhances the growth of hematopoietic progenitors in culture and modulate their engraftment activity. We aimed to characterize the hematopoietic supporting activity of OCM by comparing the secretome of immature osteoblasts to that of their precursor, mesenchymal stromal cells (MSC). Over 300 secreted proteins were quantified by mass spectroscopy in media conditioned with MSC or osteoblasts, with 47 being differentially expressed.
2020-07-17 | PXD017372 | Pride