MicroRNA expression profiling during Adipocytic differentiation of human MSCs (hMSC-TERT)
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Nehad Alajez
PROVIDER: E-GEOD-59684 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:The study aimed to identify miRNAs expression profiles associated with growth and regression of dominant-size follicles in bovine. Follicles were collected from abattoir ovaries and their status (healthy/atretic) was assessed by measuring steroid levels and aromatase expression. Total RNA was isolated from whole follicles at different developmental stages. An heterologous microarray (Exiqon, Denmark) approach followed by RT-qPCR validation (Qiagen, UK) was used to identify and compare miRNA profiles between large healthy follicles (diameter, 13M-bM-^@M-^S16 mm, n=6) and each of small (4M-bM-^@M-^S8 mm, n=6 pools of follicles) and large atretic folllicles (13-16 mm, n=6). RNA from the above groups was hybridized to the miRCURY LNAM-bM-^DM-" microRNA Hi-Power Labeling Kit,Hy3M-bM-^DM-"/Hy5M-bM-^DM-" (Exiqon) and hybridized on the miRCURY LNAM-bM-^DM-" microRNA Array (6th gen). A total of 17 and 57 microRNAs were differentially expressed (> 2 fold, adj. P-value < 0.05) between Large Healthy and each of Small and Large Atretic follicles, respectively, a fraction of which corresponded to registered bovine miRNA sequences. A subset of 5 bovine miRNAs (miR-144, miR-202,vmiR-451, miR-652, miR-873) were confirmed by qPCR to be upregulated in Large Healthy follicles, were enriched in mural granulosa cells and their predicted targets mapped to genes involved in follicular cell proliferation and differentiation, suggesting an involvemet of this subset of microRNAs in ovarian follicle development. Six biological replicates per developmental stage (total of 18 samples) were used in a double dye microRNA microarray experiment. Samples were distributed among slides so that each experimental group was represented at least once in each slide. For each gene, mean normalized intensities (n= 6 biological replicates/group) were compared between follicle stages (SF vs LHF and LHF vs LAF).
2014-06-15 | E-GEOD-54692 | biostudies-arrayexpress
Project description:By employing miRCURY LNAM-bM-^DM-" microRNA Array, we have identified a subset of 21 top miRNAs that are differentially expressed between GM-BMM and M-BMM cells To know the differential expression of miRNA in mouse GM-CSF-induced bone marrow-derived macrophages (GM-BMM) vs. M-CSF-induced BMM (M-BMM)
2013-04-17 | E-GEOD-46085 | biostudies-arrayexpress
Project description:We investigated the expression profiles of microRNAs (miRNA) in 27 renal cell carcinoma (RCC) FFPE tissues (3 chRCC, 5 papRCC and 18 ccRCC), 4 upper urinary tract-urothelial cell carcinomas of the renal pelvis-ureter (UUT-UCCs) and 20 normal kidneys by using the miRCURY LNAM-bM-^DM-" microRNA Array, 6th gen (Exiqon, Woburn MA), containing capture probes that target all miRNAs for all species registered in the miRBASE version 16.0. Real-time PCR (qRT-PCR) using appropriate endogenous controls was performed in order to validate the microarray results of the 27 most differentially expressed (DE) miRNAs. We identified 434 miRNAs that were significantly deregulated in all kidney tumours compared to the normal tissues. A total of 126 miRNAs (29%) had increased expression while 303 (69.8%) had decreased expression in RCC. Out of the 434 DE miRNAs, we detected 94 co-up-regulated and 218 co-down-regulated microRNAs among chRCC, papRCC and ccRCC. Of these, 89 and 203 were co-up- and co-down-regulated between RCCs and UUT-UCCs, respectively. We detected 11, 44 and 24 up-regulated miRNAs, which were specific for ccRCC, chRCC and papRCC, respectively. Moreover, 19, 18 and 8 miRNAs were uniquelly down-regulated in ccRCC, chRCC and papRCC, respectively. We also detected 89 and 203 co-up- and co-down-regulated miRNAs between kidney cancer and UUT-UCCs. Five miRNAs were up-regulated specifically in renal tumours and 49 in UUT-UCCs, whereas 15 miRNAs were down-regulated specifically in renal tumours and 89 in UUT-UCCs, respectively. Our data validicate that expression of miRNAs tends to be down-regulated renal cell carcinomas compared with normal kidney. We used 18 ccRCC, 3 chRCC, 5 papRCC, 4 UUT-UCC, 1 undifferentiated carcinoma and 19 normal tissue samples for miRNA profiling. Total RNA (0.5 M-BM-5g) from each sample and reference was labeled with Hy3M-bM-^DM-" fluorescent label, using the miRCURY LNAM-bM-^DM-" microRNA Hi-Power Labeling Kit (Exiqon, Woburn MA). The Hy3M-bM-^DM-\"-labeled samples were hybridized to the miRCURY LNAM-bM-^DM-" microRNA Array, 6th gen (Exiqon, Woburn MA), using an Agilent hybridization SureHyb chamber and gasket slide kits. After hybridization, the microarray slides were scanned at 10 M-NM-<m using the High-Resolution Microarray Scanner (Agilent Technologies) and stored in an ozone free environment. The image analysis was carried out using the ImaGene 8.0 software (BioDiscovery, Inc., USA). Raw microarray data were filtered, background corrected and quantile normalizated. Normalized data were further extracted, pre-processed and sorted with Microsoft ExcelM-BM-.. MicroRNAs were considered to be significantly differentially expressed if they obtained a p-value<0.05 and a FDRM-bM-^IM-$0.05.
2013-06-18 | E-GEOD-48008 | biostudies-arrayexpress
Project description:The microarray contains 9360 reporters, each present four times on the microarray. In our analysis 1326 human and viral reporters were used, of which 880 are unique human mature microRNAs. The other 8024 reporters represent microRNAs from other species. cDNA was generated using 1 M-NM-<g of total RNA per sample. RNA was labeled only with Hy3 containing dye using the microRNACURY LNAM-bM-^DM-" microRNA Hy3 Power labeling kit (Exiqon, Denmark) according to the manufacturerM-bM-^@M-^Ys protocol in a total volume of 25 M-NM-<l. To adjust the volume to 100 M-NM-<l, a hybridization buffer provided in miRCURY LNAM-bM-^DM-" microRNA Array, 5th generation kit (Exiqon, Denmark) was used. For each biological experiment, one hybridization per time point was conducted and one sample per array. In total, 24 arrays were used for 8 different conditions (BaP or control, at 6, 12, 24 and 48 hours).
2012-08-06 | E-GEOD-31252 | biostudies-arrayexpress
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2012-12-05 | E-GEOD-42722 | biostudies-arrayexpress
Project description:Follicular dendritic cells (FDC) are important stromal cells within the B cell follicles and germinal centres (GC) of secondary lymphoid tissues. FDC trap and retain native antigens on their surfaces in the form of immune complexes which they display to B cells, in order to select those cells with the highest antigen affinity. MicroRNAs are short, non-coding RNAs of approximately 18-25 nucleotides in length that regulate gene expression at the post-transcriptional level by repressing the translation of target genes. In the current study in vivo and in vitro systems were used to identify microRNAs that are differentially expressed as a result of FDC depletion. Constitutive lymphotoxin-M-NM-2 receptor (LTM-NM-2R) stimulation is required to maintain FDC in their differentiated state. We show that the rapid de-differentiation of spleen FDC that followed LTM-NM-2R-blockade, coincided with a significant decrease in the expression of mmu-miR-100-5p, mmu-miR-138-5p and mmu-miR-2137. These microRNAs were shown to be expressed in the FDC-like cell line, FL-YB, and specific inhibition of mmu-miR-100-5p significantly enhanced expression of Il6, Ptgs1/2 and Tlr4 in this cell line. The expression of each of these genes by FDC plays an important role in regulating GC size and promoting high-affinity antibody responses, suggesting that mmu-miR-100-5p may help regulate their expression during GC reactions. C57BL/6 mice were given a single intravenous injection of 100 M-BM-5g of LTM-NM-2R to temporarily deplete their FDC. At intervals after treatment 4 spleens from each group were harvested and RNA prepared. For each group samples were pooled into 2 groups of 2 and microRNA expression levels compared. Spleens from LTb-/- mice were also analysed. One channel was used for the actual sample, the second channel was used for internal QC reference.
2014-06-20 | E-GEOD-55721 | biostudies-arrayexpress
Project description:Prolificacy related traits are of great economical interest in the pig industry. microRNAs (miRNAs) are post-transcriptional regulators of gene expression important for reproductive processes. In pigs, the roles of ovarian miRNAs during gestation remain unknown although the ovaries are essential during gestation. It has been hypothesised that ovarian miRNAs could participate during the porcine gestation and, moreover, they could influence the prolificacy levels of sows. The miRNA expression profile was compared in the ovaries of pregnant Iberian x Meishan F2 sows displaying extreme phenotypes regarding prolificacy levels defined as the number of embryos (NE) attached to the uterus at 30-32 days of gestation. miR-146a-5p and miR-142-3p were differentially expressed between high (NEM-bM-^IM-%13) and low (NEM-bM-^IM-$11) prolificacy sows. In silico functional analyses of the predicted mRNA targets for these miRNAs revealed that miR-146a-5p targets were mainly involved in the immune system response important for the establishment of the maternal-foetal tolerance, implantation and maintenance of pregnancy. On the other hand, miR-142-3p targets participated in different biological processes that would contribute to the homeostasis maintenance to ensure a correct functional development of the ovaries. miRNAs associated with prolificacy levels could regulate negatively, by a novel post-transcriptional mechanism, their predicted mRNA targets, PPM1K, TLR1 and CPEB2 which have been reported as differentially expressed in the ovaries of pregnant sows regarding the prolificacy levels. Furthermore, among predicted mRNA targets for miRNAs associated with prolificacy, four genes, differentially expressed in the ovaries of pregnant sows regarding prolificacy levels, (LRRK1, BAT1, CPEB2, CCL8) are proposed to be good candidate genes for litter size due to their location within confidence intervals for prolificacy QTL described previously. Overall, it is suggested that the up-regulation of miR-146a-5p and miR-142-3p in the ovaries of pregnant sows could help in the establishment of a uterine environment, which would favor the embryonic development. Total RNA was isolated from uterus of Iberian x Meishan F2 pregnant sows divided into two groups: High prolificacy sows (n=3) and Low prolificacy sows (n=3). RNA was labeled with the Cy3-like Hy3M-bM-^DM-" dye, mixed with a pool of RNA from the six samples labeled with the Cy5-like Hy5M-bM-^DM-" dye, and hybridized to two-color miRCURYM-bM-^DM-" arrays from ExiqonM-BM-..
2012-12-01 | E-GEOD-41068 | biostudies-arrayexpress
Project description:Introduction: Circulating microRNAs (miRNAs) exhibit remarkable stability and may serve as biomarkers in several clinical cancer settings. The aim of this study was to investigate changes in the levels of specific circulating miRNA following breast cancer surgery and evaluate whether these alterations were also observed in an independent data set. Methods: Global miRNA analysis was performed on prospectively collected serum samples from 24 post-menopausal women with estrogen receptor-positive early-stage breast cancer before surgery and 3 weeks after tumor resection using global LNA-based quantitative real-time PCR (qPCR). Results: Numbers of specific miRNAs detected in the samples ranged from 142 to 161, with 107 miRNAs detectable in all samples. After correction for multiple comparisons, 3 circulating miRNAs (miR-338-3p, miR-223 and miR-148a) exhibited significantly lower, and 1 miRNA (miR-107) higher levels in post-operative vs. pre-operative samples (p<0.05). No miRNAs were consistently undetectable in the post-operative samples compared to the pre-operative samples. Subsequently, our findings were compared to a dataset from a comparable patient population analyzed using similar study design and the same qPCR profiling platform, resulting in limited agreement. Conclusions: A panel of 4 circulating miRNAs exhibited significantly altered levels following radical resection of primary ER+ breast cancers in post-menopausal women. These specific miRNAs may be involved in tumorigenesis and could potentially be used to monitor whether all cancer cells have been removed at surgery and/or, subsequently, whether the patients develop recurrence. 48 serum samples were prospectively collected from 24 patients with early stage breast cancer before and after surgery at Odense University Hospital. Serum was prepared within one hour of sample collection after centrifugation (2000 x g; 10 min at 20 M-BM-:C) and immediately stored at -80 M-BM-:C.
2014-11-01 | E-GEOD-57661 | biostudies-arrayexpress
Project description:Expression profiles of microRNAs in neonatal (isolated from day0 newborn rats) and adult rat cardiomyocytes (isolated from 2month old rats) Two condition experiment; Biological replicates: 7 samples of cardiomyocytes from neonatal rats (from independent isolations); 6 samples of cardiomyocytes isolated from adult animals (from independent isolations)
2012-10-13 | E-GEOD-41537 | biostudies-arrayexpress
Project description:Results Platelets in non-diabetic patients demonstrated miRNA expression profiles comparable to previously published data. The miRNA expression profiles of platelets in diabetics were similar. Statistical analysis unveiled only three miRNAs (miR-377-5p, miR-628-3p, miR-3137) with high reselection probabilities in resampling techniques, corresponding to signatures with only modest discriminatory performance. Functional annotation of predicted targets for these miRNAs pointed towards an influence of diabetes mellitus on mRNA processing. Conclusions/interpretation We did not find any major differences in platelet miRNA profiles between diabetics and non-diabetics. Minor differences pertained to miRNAs associated with mRNA processing. Thus, previously described differences in plasma miRNAs between diabetic and nondiabetic patients cannot be explained by plain changes in the platelet miRNA profile. Platelet miRNA profiles were assessed in clinically stable diabetic and nondiabetic patients (each n=30). Platelet miRNA was isolated from leucocyte-depleted platelet-rich plasma, and miRNA profiling was performed using LNA micro-array technology (miRBase 18.0, containing 1,917 human miRNAs). Effects of diabetes mellitus were explored by univariate statistical tests for each miRNA, adjusted for potential confounders, and by developing a multivariable signature, which was evaluated by resampling techniques. Platelet phenotype was assessed by light transmission aggregometry and impedance aggregometry.
2014-03-14 | E-GEOD-44093 | biostudies-arrayexpress