WBERRABAH
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER:
PROVIDER: E-MTAB-1743 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:To identify genes regulated by FXR in GLUTag cell line, we compared gene expression profiles in GLUTag cells treated for 24h by 0.1% DMSO and by 5M-5M GW4064
2015-06-21 | E-MTAB-2199 | biostudies-arrayexpress
Project description:This experiment uses probes designed to test the influence of various sequence-specific factors on the obtained signal intensities. The factors tested are GC content, distance from the 3'-end of the transcript, occurrence of G-quadruplexes, T7 spacer motif used in oligo-dT primers, and occurrence of (A)n motifs in the transcript sequence. The hybridization was performed using RNA isolated from two cell lines L1236 and HCT116 with 8 replicates each.
2022-11-20 | E-MTAB-12450 | biostudies-arrayexpress
Project description:The circadian clock has been found to be associated with various diseases. We showed that 5/6 nephrectomy (5/6Nx) Clk/Clk mice, which show mutation in the gene encoding circadian locomotor output cycles (Clock) do not show aggravation of renal fibrosis because transforming growth factor-1 (Tgf-1) expression is not increased. In wild-type 5/6Nx kidneys, we found that retinoid, a metabolite of retinol, led to alteration of the expresion 24-h rhythm of Clock expression. Renal Tgf- 1 expression is activated by Clock and further aggravates renal dysfunction by causing fibrosis. We also showed that, in 5/6Nx mice fed a retinol-free diet, renal fibrosis and apoptosis are reduced, leading to a marked improvement in serum creatinine levels. Moreover, our study identified hepatic Cyp3a11 and Cyp26a1 as key retinol metabolism-related genes whose expression decreased in 5/6Nx mice. Our data indicated that the negative chain reaction of metabolic clock alteration in between the kidney and liver aggravates renal dysfunction. Differential gene expression between retinol (-) feeding and clock mutant in 5/6 nephrectomized mouse was measured on the kidney at 8 weeks after operation. Four-week-old male ICR mice (Charles River Japan, Inc., Yokohama, Japan) were housed in a light-controlled room (lights on from Zeitgeber time [ZT] 0 to ZT12) at 24 ± 1°C and 60 ± 10% humidity, with food and water available ad libitum. Mice were synchronized to the lighting conditions for 2 weeks before surgery. Male ICR mice (5 weeks old) were purchased from Charles River Japan, Inc. (Kanagawa, Japan). Clock mutant mice (C57BL/6J-ClockmlJt/J) were purchased from The Jackson Laboratory (Bar Harbor, ME, USA). We placed them in the ICR genetic background to enhance breeding robustness and care of the young. These mice were backcrossed using a Jcl:ICR background for more than eight generations. We prepared mouse models of CRF by 5/6Nx operation (Ope) under sodium pentobarbital (40 mg/kg, i.p.) or diethyl ether anesthesia. 5/6Nx was performed in two stages. In the first surgical procedure (at 6 weeks of age), two-thirds of the left kidney was removed by cutting off both poles. Seven days later, the right kidney was completely removed. After the operation, mice were housed for 8 weeks (until they were 16 weeks old) in order to achieve CRF. Sham-operated (Sham) mice were subjected to laparotomy on the same days as the procedure in the 5/6Nx mice. This method was also used for treating Clk/Clk mice. Retinol-free food (A minus) was purchased form KBT ORIENTAL CO., LTD. To investigate the influences of retinol-free feeding on kidney, mice were fed from the fourth week to the eighth week after an operation.
2014-06-06 | E-GEOD-57799 | biostudies-arrayexpress
Project description:Controlling metastatic lesions is an important part of improving cancer prognosis, in addition to controlling the primary lesion. There have been many histological examinations of primary and metastatic lesions, but little basic research using cell strains from primary and metastatic lesions belonging to the same patient. In this study, we successfully established a cell strain derived from lower gingival carcinoma (WK2) and a strain derived from secondary cervical lymph node metastasis (WK3F) through primary cultures of tissue from a patient with oral squamous cell carcinoma. We then investigated the biological characteristics of the cancer cell strains from these primary and metastatic lesions, and analyzed metastasis-related genes. Comparing the biological characteristics in vitro showed WK3F to have higher cell proliferation ability and shorter cell doubling time than WK2. It also showed increased cell migratory ability, and high invasive and self-replication abilities. Heterotransplantation into nude mice resulted in high tumor formation rates in the tongue and high metastasis rates in the cervical lymph nodes. Changes in WK2 and WK3F gene expression were comprehensively analyzed with the microarray method. Genes with increased expression in WK3F compared to WK2 were extracted when Z-score ≥ 2.0 and ratio ≥ 5.0, while genes with reduced expression in WK3F compared to WK2 were extracted when Z-score ≤ -2.0 and ratio ≤ 0.2. As a result, differences were found in 604 genes. From these, MAGEC1 (88.0 times), MMP-7 (18.6 times), SNAI1 (6.6 times), MACC1 (6.2 times), and HTRA1 (0.012 times) were selected as metastasis-related candidate genes. The results suggest that these molecules could be important to clarifying the mechanism of metastasis, and could become therapeutic targets. We successfully established a cell strain derived from lower gingival carcinoma (WK2) and a strain derived from secondary cervical lymph node metastasis (WK3F) through primary cultures of tissue from a patient with oral squamous cell carcinoma. Changes in WK2 and WK3F gene expression were comprehensively analyzed with the microarray method.
2014-06-30 | E-GEOD-54672 | biostudies-arrayexpress
Project description:Blue mussel larvae were fed, in a first group, a balanced diet of essential fatty acids (EFAs) provided by a cocktail diet (COC) from three algal species. Larvae were cultured in three separate tanks from hatching, 0 day post-fertilization (DPF) until 42 DPF. Treated larvae were fed a deficient diet (Tiso) that contains low levels of arachidonic acid (AA) and eicosapentaenoic acid (EPA), two EFAs necessary for larval development, performance, and survival. The goal is to identify coordinated patterns of gene expression and understand their predictive function in relation to growth and mortality during early developmental stages of the blue mussel Mytilus edulis. In order to understand the mechanisms by which growth and survival drive an organism to the full range of its adaptation, we de novo assembled of the mussel transcriptome during early development using next-generation sequencing (NGS) technology, then designed customized microarrays targeting every developmental stage, which encompass major transitions in tissue organization of the fast-evolved blue mussel Two experimental conditions, COC and Tiso diets. Biological replicates 3 culture replicate per stage of development for 5 stages of development. Eggs and trocophore larvae did not undertake treatments
2014-08-31 | E-GEOD-55580 | biostudies-arrayexpress
Project description:To characterize gene expression changes in mice following serous retinal detachments, we employed whole genome microarray expression profiling as a tool to identify genes with the potential effects on the neural retina as well as retinal pigmented epithelium. Total RNA was harvested from nm3342 (mutant) and age-matched wild-type (C57Bl/6J) mice at P30 or P365 for examination using microarray analysis. Retinas and retinal pigmented epithelium was harvested from both age-matched mutant and wild-type mice.
2015-05-16 | E-GEOD-68961 | biostudies-arrayexpress
Project description:We provide an original multi-stage approach identifying a gene signature to assess the fibroblast polarization. Prototypic polarizations (inflammatory/fibrotic) were induced by seeded mouse embryonic fibroblasts (MEFs) with TNFα or TGFß1, respectively. The transcriptomic and proteomic profiles were obtained by RNA microarray and LC/MS-MS. Gene Ontology and pathways analysis were performed among the differentially expressed genes (DEGs) and proteins (DEPs). Balb/c mice underwent daily intradermal injections of HOCl (or PBS) as an experimental murine model of inflammation-mediated fibrosis in a time-dependent manner. As results, 1,456 and 2,215 DEGs, and 289 and 233 DEPs were respectively found in MEFs in response to TNFα or TGFß1, respectively. Among the most significant pathways, we combined 26 representative genes to encompass the proinflammatory and profibrotic polarizations of fibroblasts. Based on principal component analysis, this signature deciphered baseline state, proinflammatory polarization, and profibrotic polarization as accurately as did RNA microarray and LC/MS-MS. Then, we assessed the gene signature on dermal fibroblasts isolated from the experimental murine model. We observed a proinflammatory polarization at day 7, and a mixture of a proinflammatory and profibrotic polarizations at day 42 in line with histological findings. Our approach provides a small-size and convenient gene signature to assess murine fibroblast polarization.
2022-07-12 | PXD034078 | Pride
Project description:In addition to their role as a digestive detergent, bile acids have the ability to modulate the expression of genes. The intestinal content of cholic acids (CA) fluctuated in response to the daily feeding-fasting cycle; therefore, we hypothesized that the temporal accumulation of CA may affect the expression of genes in intestinal epithelial cells. To screen bile acid-regulated genes, we performed oligonucleotide microarray analyses using RNA isolated from the CA-treated intestinal cells of mice. Several types of genes were screened as candidates for bile acid-regulated genes. They included genes that encoded lipid metabolism-related proteins, receptors, transcriptional factors, and plasma-membrane transporters. Total 2 samples were derived from [1] vehicle (0.05% DMSO and 0.25% ethanol)-treated intestinal epithelial cells of mice and [2] cholic acid (CA)-treated intestinal epithelial cells of mice.
2015-08-01 | E-GEOD-55443 | biostudies-arrayexpress
Project description:In order to determine molecular mechanisms of faster skin wound healing under decreasing FoxO1 protein expression, we performed microarray analysis on 3 days skin wounded samples from FoxO1+/- and WT mice. Skin wound-induced gene expression in WT and FoxO1+/- mice were measured on 3 days after injury. Three independent experiments were performed at each mouse.
2014-06-01 | E-GEOD-48473 | biostudies-arrayexpress
Project description:CSE knockout (CSE-KO)mice at age 6 months were fed a high fat diet (HFD) for 8 weeks.we determined the effects of CSE knockdown on beta-cell function and mass in islets from the mice. After 8 weeks of the HFD,blood glucose levels were drasically increaced in CSE-KO mice compared with WT mice. To assess the effect of HFD on gene expression in CSE-KO mice,we performed a comparative DNA microarray analysis 2 samples analysis.control is CSE-WT(HFD+)
2013-09-02 | E-GEOD-50458 | biostudies-arrayexpress