Effect of polyphosphates on osteoblast mineralization
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ABSTRACT:
ORGANISM(S): Rattus norvegicus
SUBMITTER: yoshikazu mikami
PROVIDER: E-GEOD-79176 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Rat osteoblasts ROB17/2.8 cells were cultured in the presence of high (1mg/ml) or low (0.01mg/ml) concentration of polyphosphates.
2016-03-15 | GSE79176 | GEO
Project description:In the present study, the Agilent-016251 Sparus aurata oligo microarray platform (GEO accession: GPL6467) was used to compare expression profiles of mineralization-induced VSa16 cell cultures against untreated ones. ECM mineralization was induced for 4 weeks by supplementing medium with 50 µg/ml of L-ascorbic acid, 10 mM β glycerophosphate and 4 mM CaCl2. For each group, total RNA was extracted from three (3) independent biological replicates, each consisting of pools of cells. Data analysis demonstrated that expression profiles were strongly affected by ECM mineralization with hundreds of genes differentially expressed with relevant fold-change. In this study, we analyzed six (6) cell samples, three (3) collected from untreated VSa16 cell cultures and three (3) collected from mineralization-induced VSa16 cell cultures. Gene expression profiling was performed using Agilent-016251 Sparus aurata oligo microarray platform (GPL6467) (6 arrays, no replicate) based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 microns; all slides were scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software created a unique ID for each pair of XDR scans and saved it to both scan image files. Feature Extraction (FE) 9.5 used XDR ID to link the pairs of scans together automatically when extracting data. The signal that was left after all the FE processing steps was ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal.
2011-06-01 | E-GEOD-18941 | biostudies-arrayexpress
Project description:Aim of the study was to characterize at a molecular level (changes in transcriptomes) the effect of monosodium urate crystal (MSU) on HaCaT keratinocyte cell line. This was adressed by using a culture model. The HaCaT cell line (human keratinocytes) was stimulated by MSU (1mg/mL) vs control for 12 hrs. By using genome-wide expression profiling, we identified deregulation of functionally relevant gene networks. HaCaT were obtained from Cell Lines Service (Eppelheim, Germany) and grown in DMEM medium (PAN biotech, Aidenbach, Germany) supplemented with 10% FBS (Life Technology, Grand Island, NY, USA), L-glutamine and non-essential amino acid. Before the treatment HaCaT cells were cultured in serum-free medium for 12hrs. HaCaT were treated with MSU (1mg/ml) vs DMEM control for 12hrs then submitted to RNA extration and gene expression profiling. Triplicate experiments were performed: HaCaT control (n=3), MSU-treated (n=3).
2015-10-29 | E-GEOD-65931 | biostudies-arrayexpress
Project description:Gene expression profiling of the rat lung following intratracheal instillation with C60 fullerene particles was employed to gain insights into these molecular events. Groups of nine-week-old male Wistar rats (n= 4-6 per group/ time point) were intratracheally instilled with C60 fullerene suspended in 0.4 ml distilled water including 0.8% Tween-80 as a single injection (0.1 mg, 0.2 mg (LD: low doses) and 1.0 mg (HD: high dose) C60 fullerene/ rat). Control groups received 0.8 % Tween-80 (vehicle control). After intratracheal instillation treatment, rats were housed within polycarbonate cages at a controlled temperature of 22 °C with a chow diet ad libitum, and dissected at 3 days, 1 week, 1 month, 3 month, and 6 month post-instillation. Right lungs of anesthetized rats were perfused with physiological saline, excised, and used for DNA microarray analysis.
2009-08-26 | E-GEOD-17747 | biostudies-arrayexpress
Project description:To further development of our gene expression approach to assess the effects of manufactured nanomaterials at the transcriptional level, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to distinguish characterization of physicochemical properties of impurity-free single-wall carbon nanotubes (SWCNTs). We have prepared two types of dispersed the SWCNTs, namely relatively small bundles and a short linear shape (CNT-1) and large bundles and a long linear shape (CNT-2), and attempted to characterize time-dependent changes in the gene expression of lung tissues until 90 days after intratracheal instillation with SWCNTs suspensions at 0.4 mg injected dose per rat. Groups of nine-week-old male Wistar rats (n= 4 per group/ time point) were intratracheally instilled with single-wall carbon nanotubes (SWCNTs) suspended in 0.4 ml of 1.0mg/mL bovine serum albumin (BSA) as a single injection 0.4 mg SWCNTs/ rat. Control groups received 1.0mg/mL BSA (vehicle control). After intratracheal instillation treatment, rats were housed within polycarbonate cages at a controlled temperature of 22 M-BM-0C with a chow diet ad libitum, and dissected at 1day, 3 days, 7 days, 30 days, and 90 days post-instillation. Right lungs of anesthetized rats were perfused with physiological saline, excised, and used for DNA microarray analysis.
2014-09-17 | E-GEOD-61483 | biostudies-arrayexpress
Project description:Transcriptional profile of C. elegans comparing control vs. nematodes treated with 0.5 mg/ml of Chlorpyrifos and 1mg/ml of Diazinon (DZN) at 16°C. Toxicant was added to agar and nematode culture on petri dishes for 72h before harvesting.
2010-07-22 | GSE16698 | GEO
Project description:Gene expression profiling of the rat lung following intratracheal instillation with SWCNTs was employed to gain insights into these molecular events. We attempted to characterize time-dependent changes in the gene expression until 754 days after intratracheal instillation with SWCNTs suspensions at 0.2 mg (L-SWCNT) and 0.4 mg (H-SWCNT) injected dose per rat, and to identify the shift from the acute-phase to the chronic-phase phase on the basis of evaluation at the molecular level. Groups of nine-week-old male Wistar rats (n= 6 per group/ time point) were intratracheally instilled with single-wall carbon nanotubes (SWCNTs) suspended in 0.4 ml distilled water including 0.1% Triton X-100 as a single injection 0.1 mg (L-SWCNT) and 0.4 mg (H-SWCNT) SWCNTs/ rat). Control groups received 0.1% Triton X-100 (vehicle control). After intratracheal instillation treatment, rats were housed within polycarbonate cages at a controlled temperature of 22 M-BM-0C with a chow diet ad libitum, and dissected at 3 days, 7 days, 30 days, 90 days, 180 days, 365 days and 754 days post-instillation. Right lungs of anesthetized rats were perfused with physiological saline, excised, and used for DNA microarray analysis.
2013-09-07 | E-GEOD-50664 | biostudies-arrayexpress
Project description:To further development of our gene expression approach to assess the effects of manufactured nanomaterials at the transcriptional level, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to distinguish characterization of physicochemical properties of single-wall carbon nanotubes (SWCNTs). Two kinds of the impurity-free singlewall carbon nanotubes (SWCNTs), CNT-1 or CNT-2 induced gene expression in rat alveolar macrophages were measured at 24 hours exposure to doses of 0.1mg/mL. The experiments were performed using control for each experiment (n=4).
2014-09-11 | E-GEOD-61319 | biostudies-arrayexpress
Project description:8-oxoguanine (8-oxoG) is one of the most common DNA lesions generated by reactive oxygen species. Here we show the genome-wide distribution of 8-oxoG by coupling immunoprecipitation by antibodies specific for the DNA fragments containing 8-oxoG with microarray that covers rat genome. Genome-wide mapping of 8-oxoG in rat kidney reveals that 8-oxoG preferentially located at gene deserts and depleted in genic regions. We did not observe the difference in 8-oxoG level between highly- and lowly-expressed groups of genes, may be because of the low level of 8-oxoG in genic regions in general comparing to gene deserts. Rather, the distribution of 8-oxoG highly correlates with the distribution of lamina associated domains (LADs), suggesting that the spatial location of the genomic regions in the nucleus is the major determinant for the susceptibility to oxidative modifications. One possible explanation for the enrichment of 8-oxoG in LADs is that the nuclear periphery is more susceptible to the oxidative damage coming from outside the nucleus. Another explanation is that LADs take rather compact conformation, which might prevent the recruitment of the repairing complex to the modified bases. Normal condition. Biological replicate 2
2014-01-13 | E-GEOD-54007 | biostudies-arrayexpress
Project description:Transcriptional profile of C. elegans comparing control vs. nematodes treated with 1mg/ml of Diazinon (DZN) at 16°C. Toxicant was added to agar and nematode culture on petri dishes for 72h before harvesting.
2010-07-22 | GSE16686 | GEO