Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA209506 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Osteosarcoma (Osteosarcoma) is a type of bone cancer. Eighty percent of this tumor will be metastatic to the lungs or liver, and as a result, patients generally need chemotherapy to improve survival possibility. Recently, anti-tumor activity has been reported in Ocimum gratissimum aqueous extract (OGE), which has been the focus of recent extensive studies on therapeutic strategies due to its antioxidant properties. We used microarrays to identify potential and novel target genes responsive to the anticancer effect in OGE treatment in osteosarcoma cells, We performed pharmacogenomics analyses for the effect of OGE on human osteosarcoma U2-OS and HOS cell growth. Cell viability, Western blot and flow cytometry analysis were performed before performing pharmacogenomics analyses for the effect of OGE on human osteosarcoma U2-OS and HOS cell growth, including cDNA microarray and RT-PCR assays.
2013-06-26 | E-GEOD-48281 | biostudies-arrayexpress
Project description:Analysis of two metastatic OS cell lines, KHOS and KRIB, and two non-metastatic OS cell lines, HOS and U2OS. Results show differences in gene expression between cell lines with different ability to metastasise in vivo.
2013-07-19 | GSE49003 | GEO
Project description:Investigation of whole transcriptional changes in F. verticillioides FRC M-3125 when exposed to 5 μg/ml pyrrocidine A (PA), 20 μg/ml pyrrocidine B (PB), 50 μg/ml 2-benzoxazolinone (BOA), 50 μg/ml 2-oxindole (OXD), 50 μg/ml 2-coumaranone (CMN), or 50 μg/ml chlorzoxazone (CZX). Cultures were harvested one hour after exposure. Assessed in reference to control cultures of M-3125 exposed to DMSO (0.5% final concentration) since all the above compounds were dissolved in DMSO.
2019-06-25 | GSE116351 | GEO
Project description:U2-OS cells were transfected with scramble siRNA or PKC delta siRNA, then left untreated or treated with 2 ug/ml adriamycin for 8 h.
2011-03-23 | E-MEXP-2643 | biostudies-arrayexpress
Project description:Analysis of two metastatic OS cell lines, KHOS and KRIB, and two non-metastatic OS cell lines, HOS and U2OS. Results show differences in gene expression between cell lines with different ability to metastasise in vivo. Each of the four cell lines were analyzed in tripicate. Total RNA was extracted from each triplicate cell line culture with Trizol. cRNA was amplified using the Ambion Illumina Total Prep RNA Amplification Kit. Concentration was determined in NanoDrop and qulity checked in the Agilent Bioanalyzer, before hybridizing to Illumina HT-12 BeadChip Array.
2013-07-19 | E-GEOD-49003 | biostudies-arrayexpress
Project description:Background: Osteosarcoma (OS) is a very aggressive bone tumor characterized by highly abnormal complex karyotypes. With the improved resolution offered by array comparative genomic hybridization (array CGH) platforms, it is possible to readily detect cryptic microaberrations in genomic DNA. The identification of these microaberrations in genetic syndromes is currently the focus of many array CGH studies, but there have been no analyses to date documenting the occurrence of microaberrations in tumors. Results: In this study we utilized high-resolution oligonucleotide array CGH to identify novel microaberrations under ~750 kb in four OS-derived cell lines: U-2 OS, HOS, MG-63 and SAOS-2. Comparative analysis of these alterations showed that SAOS-2 harbored the most microaberrations at 17, followed by MG-63 with 11, HOS with 9 and U-2 OS with 6. SAOS-2, which has a TP53 mutation, exhibited the highest level of chromosomal instability in previous studies by our group; whereas U-2 OS, which has wild-type p53 status, exhibited the least instability. A consensus region of gain at 5p15.33 was detected in three of the four OS-derived cell lines (HOS, MG-63 and SAOS-2) by aCGH. Of these consensus gains, one was a microaberration of 500 kb in SAOS-2, and confirmed by fluorescence in situ hybridization analysis. It should be noted that this microaberration is immediately telomeric to the TERT gene, which also showed gain. TERT is correlated with increased tumor aggression, as well as decreased progression free survival in OS patients. Experiment Overall Design: This genome-wide analysis is the first study to utilize oligonucleotide array CGH to identify microaberrations in OS, likely to contain genes involved in OS tumor oncogenesis. A better understanding of the underlying molecular genetic events leading to tumor initiation and progression could result in the identification of prognostic markers and therapeutic targets.
2008-06-18 | E-GEOD-7077 | biostudies-arrayexpress
Project description:Background: Osteosarcoma (OS) is a very aggressive bone tumor characterized by highly abnormal complex karyotypes. With the improved resolution offered by array comparative genomic hybridization (array CGH) platforms, it is possible to readily detect cryptic microaberrations in genomic DNA. The identification of these microaberrations in genetic syndromes is currently the focus of many array CGH studies, but there have been no analyses to date documenting the occurrence of microaberrations in tumors. Results: In this study we utilized high-resolution oligonucleotide array CGH to identify novel microaberrations under ~750 kb in four OS-derived cell lines: U-2 OS, HOS, MG-63 and SAOS-2. Comparative analysis of these alterations showed that SAOS-2 harbored the most microaberrations at 17, followed by MG-63 with 11, HOS with 9 and U-2 OS with 6. SAOS-2, which has a TP53 mutation, exhibited the highest level of chromosomal instability in previous studies by our group; whereas U-2 OS, which has wild-type p53 status, exhibited the least instability. A consensus region of gain at 5p15.33 was detected in three of the four OS-derived cell lines (HOS, MG-63 and SAOS-2) by aCGH. Of these consensus gains, one was a microaberration of 500 kb in SAOS-2, and confirmed by fluorescence in situ hybridization analysis. It should be noted that this microaberration is immediately telomeric to the TERT gene, which also showed gain. TERT is correlated with increased tumor aggression, as well as decreased progression free survival in OS patients. Keywords: comparative genomic hybridization (array CGH)
2007-12-31 | GSE7077 | GEO
Project description:Background Osteosarcoma (OS) is the most common malignant bone tumor in children and adolescents. The survival rate of patients with metastatic disease remains very dismal. Nevertheless, metastasis is a complex process and a single-level analysis is not likely to identify its key biological determinants. In this study, we used a systems biology approach to identify common metastatic pathways that are jointly supported by both mRNA and protein expression data in two distinct human metastatic OS models. Results mRNA expression microarray and N-linked glycoproteomic analyses were performed on two commonly used isogenic pairs of human metastatic OS cell lines, namely HOS/143B and SaOS-2/LM7. Pathway analysis of the differentially regulated genes and glycoproteins separately revealed pathways associated to metastasis including cell cycle regulation, immune response, and epithelial-to-mesenchymal-transition. However, no common significant pathway was found at both genomic and proteomic levels between the two metastatic models, suggesting a very different biological nature of the cell lines. To address this issue, we used a topological significance analysis based on a “shortest path” algorithm to identify topological nodes, which uncovered additional biological information with respect to the genomic and glycoproteomic profiles but remained hidden from the direct analyses. Pathway analysis of the significant topological nodes revealed a striking concordance between the models and identified significant common pathways, including “Cytoskeleton remodeling/TGF/WNT”, “Cytoskeleton remodeling/Cytoskeleton remodeling”, and “Cell adhesion/Chemokines and adhesion”. Of these, the “Cytoskeleton remodeling/TGF/WNT” was the top ranked common pathway from the topological analysis of the genomic and proteomic profiles in the two metastatic models. The up-regulation of proteins in the “Cytoskeleton remodeling/TGF/WNT” pathway in the SaOS-2/LM7 and HOS/143B models was further validated using an orthogonal Reverse Phase Protein Array platform. Conclusions In this study, we used a systems biology approach by integrating genomic and proteomic data to identify key and common metastatic mechanisms in OS. The use of the topological analysis revealed hidden biological pathways that are known to play critical roles in metastasis. Wnt signaling has been previously implicated in OS and other tumors, and inhibitors of Wnt signaling pathways are available for clinical testing. Further characterization of this common pathway and other topological pathways identified from this study may lead to a novel therapeutic strategy for the treatment of metastatic OS. In this study we analyzed two human metastatic OS cell lines and their parental non-metastatic lines. The two human metastatic OS cell line models were HOS/143B and SaOS-2/LM7. The HOS cell line, originally known as M.T. and later as TE-85, was derived from an OS of a 13 year-old girl. The 143B metastatic subline was generated from HOS by a Ki-RAS oncogene transformation [Rhim, J.S., et al., Characterization of human cells transformed in vitro by N-methyl-N'-nitro-N-nitrosoguanidine. Int J Cancer, 1977. 19(4): p. 505-10.]. The SaOS-2 cell was derived from an OS of an 11 year-old girl, and its metastatic subline LM7, was developed by multiple in vivo selection of SaOS-2 cells in mice with pulmonary metastases [Jia, S.F., L.L. Worth, and E.S. Kleinerman, A nude mouse model of human osteosarcoma lung metastases for evaluating new therapeutic strategies. Clin Exp Metastasis, 1999. 17(6): p. 501-6.]. No replicates were included.
2012-04-24 | E-GEOD-37552 | biostudies-arrayexpress
Project description:Transcriptional profiling to investigate the effect of drug treatment on the E. faecalis cells. For microarray analysis, E. faecalis OG1RF was grown in FMC medium supplemented with 10 mM glucose to an optical density at 600 nm (OD600) of 0.3 and the cultures were divided in 7 aliquots. One aliquot was collected by centrifugation and immediately frozen (untreated control cells). The other aliquots were treated for 30 or 60 min with 1.25 X the minimum inhibitory concentration (MIC) of one of the following CW inhibitors: ampicillin (20 μg ml-1), bacitracin (80 μg ml-1), or cephalothin (80 μg ml-1). After an exposure time of 30 or 60 minutes, each of these cultures was also centrifuged and the pellets frozen. RNA was then isolated from each pellet for microarray analysis. This process was repeated 3 additional times, for a total of four replicates of each condition.
2013-03-16 | GSE45231 | GEO
Project description:Transcriptomic changes in iPSC-derived hepatocytes after exposure to varying concentrations of AgNPs (0.01-25 μg/ml) for 24 h.
2024-06-21 | GSE259384 | GEO