Global gene expression changes associated with miR-375 overexpression
ABSTRACT: To determine gene expression changes assoicated with miR-375 overexpression, MCC26 (merkel cell carcinoma cell line) were transfected with 5nM of miR-375 mimics. RNA was isolated 72 hours post-transfection and subjected to gene expression analysis using Agilent human 4X44 whole genome microarrays. Analysis was performed on microarray data corresponding to two independent experiments (n=2) Overall design: 5nM of mirVana miR-375 or neg cntrl mimics (Invitrogen) was transfected into MCC26 cells using lipofectamine 2000. Cells apporimately 30% confluence when transfected and RNA was collected 72 hours post-transfection. miR-375 overexpression was confirmed, and then RNA was subjected to whole genome microarray analysis using Agilent human 4x44 chip. Experiment was repeated (n=2).
INSTRUMENT(S): Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Probe Name version)
Project description:To identify the direct target of miR-490-3p, we used whole genome microarray expression profiling to screen for genes potentially regulated by the microRNA. AGS cells were transfected with control mimics or miR-490-3p mimics and gene expression was determined 72 hours after transfection.
Project description:We investigated the functional significance of ASH1-inducible miR-375 in terms of biologic phenotypes of ASH1-positive lung cancer cells. To this end, we conducted genome-wide expression profiling analysis of miR-375-transfected A549 cells. Microarray analysis using a Whole Human Genome 4 x 44K Microarray G4112F (Agilent) was conducted to examine changes in expression of potential target genes of miR-375 by transfection of Pre-miR-375 or Pre-miR-NC#2 (Ambion) in A549 cells, which were then harvested at 12, 24, 48, and 96 hours after transfection.
Project description:Our work demonstrated that PPAR-α regulates miR-7, a microRNA which regulates SREBP1 signaling. We used microarrays to detail the effect of miR-7 on hepatic gene expression, and, within activated genes, identified an enrichment for genes with SREBP1 binding sites in their promoters. Overall design: Huh7.5 cells were transfected with miR-7 or control mimics (100 nM), and total RNA was isolated 72 hours post-transfection.
Project description:In this study, we comparatively analyzed the members of the miR-449 family (miR-449a, miR-449b, and miR-449c) with regards to their target genes and functional effects in hepatocellular carcinoma (HCC). Microarray analysis after transient transfection of miR-449a, miR-449b, and/or miR-449c in the HCC cell line HLE identified putative target genes of miR-449a, miR-449b, and miR-449c. For transient overexpression of miRNAs, the HCC cell line HLE was transfected with 50 nM Allstars Negative Control or miScript miRNA mimics. MiRNA mimics for miR-449a, miR-449b, and miR-449c were either single transfected or cotransfected in equimolar amounts (16.7 nM each). Global mRNA expression profiling was performed utilizing pooled RNA of three biological replicates per microarray and two microarrays per condition.
Project description:RAW264.7 mouse macrophages were transfected with negative control and miR-342-3p mimics and subjected to microarray analysis 18 hours after the transfection. We used microarray to obtain global mRNA expression data of negative control and miR-342-3p mimics-transfected RAW264.7 cells. Overall design: RAW264.7 mouse macrophages were transfected with negative control and mir-342-3p mimics. The global mRNA expression patterns of negative control and miR-342-3p mimics-transfected RAW264.7 cells were analyzed on Affymetrix microarrays.
Project description:Our work demonstrated that 25-hydroxycholesterol induces the expression of miR-185, a microRNA which reinforces the oxysterol's antiviral effects on hepatic metabolism. We used microarrays to detail the effect of miR-185 on hepatic gene expression, and, within repressed genes, identified an enrichment for genes associated with cholesterol biosynthesis. Overall design: Huh7.5 cells were transfected with miR-185 or control mimics (100 nM), and total RNA was isolated 72 hours post-transfection.
Project description:To identify targets post-transcriptionally regulated by miR-100 and miR-125b, we have performed AGO2 RIP-seq and RNA-seq following overexpression of the two miRNAs in PANC-1 cells. In addition, we have carried out RNA-seq following TGFb stimulus to evaluate changes in gene expression driven by TGFb. Overall design: For AGO2 RIP-seq and RNA-seq PANC-1 cells were transfected with precursor miRNA mimics for miR-100, miR-125b and negative control (0.5nM) for 24h. The experiment was performedin two biological replicates. For evaluation of changes in gene expression driven by TGFb PANC-1 cells were treated with TGFb (5nM) or vehicle control for 72h. Three biological replicates for each condition were used for expression analysis.
Project description:The mouse mSCC-20 cell line was transfected with 5nM of mmu-pre-miR-193b-3p, pre-miR-365a-3p or pre-miR-NC1. Total RNAs were extracted 30 h after transfection and hybridized on microarrays. One color experiment with 3 experimental conditions : miR-NC1- (n=4), miR-193b-3p- (n=2) and miR-365-3p- (n=2) transfected cells, corresponding to a total of 8 samples.
Project description:The mouse mSCC-20 cell line was transfected with 5nM of mmu-pre-miR-193b-3p, pre-miR-365a-3p or pre-miR-NC1. Total RNAs were extracted 30 h after transfection and hybridized on microarrays. Overall design: One color experiment with 3 experimental conditions : miR-NC1- (n=4), miR-193b-3p- (n=2) and miR-365-3p- (n=2) transfected cells, corresponding to a total of 8 samples.
Project description:The global microRNA (miRNA) profiling expression was assessed in a large series of both sporadic and hereditary forms of medullary thyroid carcinomas (MTC), and to evaluate the biological function of major found altered miRNAs. For this purpose we investigated miRNA differential expression in tumoral vs adjacent non tumoral tissues from 62 MTC patients, and showed a specific overexpression of miR-375, -129-3p, -376c, -335, -96, -10a, -7, -429 and an underexpression of miR-451 in tumoral tissues. Since miR-375 was the most up-regulated miRNA, we thus decided to identify its targets by combining a transcriptomic signature of cells transfected either with premiR- or antagomiR-375 and an in silico analysis joining TT-cells mRNA specific signature from Cancer Cell Line Encyclopedia GEO dataset and miRNA prediction algorithms. Using this restrictive approach, we focused on miR-375 target SEC23A and validated a decreased expression of SEC23A by Western blotting and by immunohistochemistry in tumoral vs non tumoral adjacent thyroid epithelium. Furthermore, we observed that overexpression of miR-375 was associated with decreased proliferation and increased vandetanib response in vitro. Overall, our results showed an overexpression of miR-375 in MTC in association with a decrease of miR-375-potential targets including SEC23A. Additionnally, we postulate thatmiR-375 overexpression should be evaluated in MTC patients treated with the tyrosine kinase inhibitor, vandetanib. Overall design: 2 cell lines: TT and ORI (Nthy ORI 3.1) transfected with the antagomir-375 and premir-375 respectively. For each condition a control condition was provided. A total of 4 conditions: 2 transfections and their 2 respective controls are analyzed. For each condition 2 replica are provided. A total of 8 samples are submitted in this dataset.