Microarray analysis of the NK92MI cell line treated with CD200 peptide at 2hr and 4hr timepoints compared to untreated
Ontology highlight
ABSTRACT: We used RNA microarray to investigate CD200-mediated apoptosis on the NK92MI celll line. We aimed to identify apoptotic gene signatures. RNA was extracted from NK92MI cells and sent for sequencing. raw sequencing data was then processed in R using 'lumi' and 'limma' packages.
Project description:We used RNA microarray to investigate the expression of full-time and part-time sheddases and their substrates in basal cell carcinoma when compared to squamous cell carcinoma and normal skin. We aimed to identify the involvement of these sheddases in CD200 ectodomain shedding. RNA was extracted from whole primary tissues and sent for sequencing. raw sequencing data was then processed in R using 'lumi' and 'limma' packages.
Project description:The aim of this study is to establish a comprehensive transcriptome atlas that enables identification of key molecular pathways and morphogenic events regulating postnatal renal medulla/papillary and cortex development. To achieve this, a microarray expression profiling was performed on postnatal day 0-90 renal medulla and cortex obtained from CD1 male mice. Renal medulla and cortex were regionally dissected from postnatal day 0-90 CD1 male mice, and total RNA extracted for microarray expression profiling. Each time point consists of RNA pooled from 4 biological replicates, and an Agilent Bioanalyser test was performed to assess RNA integrity prior to sample pooling. The microarray data was analysed with the use of lumi and limma packages (Bioconductor) in R.
Project description:Comparison of gene expression profiles of mouse bone marrow nucleated cells. All comparisons are made between biological replicates (different mice) derived from animals carrying the Type A cytoplasmic Nucleophosmin mutation (Npm1c) found in human Acute Myeloid Leukaemia. Mice were culled 8 weeks after induction of the conditional Npm1c allele with Mx1-Cre. Whole bone marrow (BM, n=20: 11xNpm1c & 9xWildType) or antibody purified cell fractions (Lin minus, n=6: 4xNpm1c & 2xWildType; B220+, n=5: 3xNpm1c & 2xWildType and Gr1+/Mac1+, n=6: 4xNpm1c & 2xWildType) were studied. Files ("samples") include data from all samples in each comparison.<br>Global profiling was done using Illumina mouse-6 expression beadchip version 2. Data were quantile normalised and analysed using the bioconductor (http://www.bioconductor.org/), lumi (http://www.bioconductor.org/packages/2.0/bioc/html/lumi.html ) and limma packages, then p-value adjusted for multiple testing.
Project description:Genome-wide expression profiling of stably NGFR transfected melanoma cells was used to identify genes driven by expression of the nerve growth factor receptor CD271 (NGFR). Stable overexpression of NGFR (CD271): Generation of cell lines stably overexpressing CD271 (NGFR), melanoma cells were transfected with 2 µg of a plasmid expressing GFP-tagged human NGFR (RG207966, OriGene) and selected with G418 (100-300 µg/ml, PAA) over a period of two weeks followed by sub-cloning or FACS. Gene expression profiling: Whole genome expression profiling of T20/02 and A375 cells (NGFR) and control cells (Mock or GFP) was performed with three biological replicates. Illumina raw data of BeadChip HumanHT-12V4 platform were summarized via the BeadStudio without normalization and background correction. Follow-up processing was done via the R/Bioconductor environment employing packages lumi, limma and q-value. Data were normalized with quantile normalization. Genes were termed significantly differentially expressed when the average detection p-value of at least one case was < 0.05 the ratio was outside the interval [0.75,1.33], one of the p-values from limma test, Student's t-test, Welch test and Wilcoxon test was < 0.05. At least one of the q-values corresponding to one of these tests < 0.05.
Project description:Analysis of early stages of alcohol dependence at the gene expression level. The hypothesis tested in the present study was that ethanol-treatment impact gene expression in a mouse model of high ethanol consumption. Results provide important information of genes and pathways being affected by ethanol actions in the mouse frontal cortex. Total RNA obtained from frontal cortex from mice treated with 20% ethanol solution for 20 days. Control group is composed of untreated animals. Frontal cortex (FCtx) tissue was dissected to produce a 2-mm coronal section from the most rostral portion of the mouse brain devoid of olfactory bulbs (coordinates Bregma +1.56 to +3.56). The dorsal part of this coronal section, cut immediately above the forceps minor of the corpus callosum as the anatomical landmark, was used for RNA extraction. This section of the cortex is mostly composed of frontal associated cortex (FrA), cingulate cortex area 1 (Cg1), prelimbic cortex (PrL), and primary (M1) and secondary (M2) motor cortices, as depicted in the mouse brain atlas (Franklin and Paxinos 2007). Samples from both alcohol-treated and control groups were always included in each batch of extracted RNA. Total RNA was extracted using the mirVanaM-BM-. miRNA Isolation kit (Ambion, Austin, TX) according to the manufacturerM-bM-^@M-^Ys instructions. Yield and quality of the total RNA preparation was determined using the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA). For mRNA expression profiling, biotin-labeled cRNA was prepared using Illumina TotalPrep RNA Amplification kit (Ambion, Austin, TX) and then hybridized to Illumina MouseRef-8 v2.0 Expression BeadChips (Illumina, San Diego, CA). The quality of the Illumina bead summary data was assessed using the Bioconductor packages Lumi and arrayQualityMetrics. Data preprocessing included variance stabilization and quantile normalization using the Lumi package. Statistical analysis comparing ethanol-treated and control groups was performed using the Bioconductor package limma, which implements an empirical Bayes approach in R (Smyth 2005). False discovery rate (FDR) was assessed using the Benjamini-Hochberg method.
Project description:Cells from SIV-negative (SIVnegative_p17, n=5; SIVnegative_p18, n=5) and SIV-chronic (ChronicSIVinfection_p18, n=6) SP tissues were sorted for microarray studies. RNA samples were prepared using the Illumina beads station assay and hybridized to the Illumina HumanHT-12 version 4 Expression BeadChip according to the Illumina’s instruction. The data were normalized with the quantile normalization method of Bioconductor package limma . Missing values were imputed with R package impute (http://cran.rproject.org/web/packages/impute/index.html). Genes with significant differential expression levels were identified using Bioconductor limma package with >= 1.5 fold change (up or down), the false discovery rate (FDR) adjusted P value < 0.05.
Project description:Cells from SIV-negative (SIVnegative_p17, n=5; SIVnegative_p18, n=5) and SIV-chronic (ChronicSIVinfection_p18, n=6) SP tissues were sorted for microarray studies. RNA samples were prepared using the Illumina beads station assay and hybridized to the Illumina HumanHT-12 version 4 Expression BeadChip according to the Illumina’s instruction. The data were normalized with the quantile normalization method of Bioconductor package limma . Missing values were imputed with R package impute (http://cran.rproject.org/web/packages/impute/index.html). Genes with significant differential expression levels were identified using Bioconductor limma package with >= 1.5 fold change (up or down), the false discovery rate (FDR) adjusted P value < 0.05. Cells from SIV-negative (SIV and SIV-chronic SP) tissues were sorted for micorarray studies
Project description:Microarray analysis was performed at the UHN Microarray Centre (UHNMAC, Ontario, Canada) using Illumina HumanHT-12 v4 BeadChip with 500 ng of total RNA prepared by RNeasy mini kit (QIAGEN, Cat. No. 74104). Samples from HCC1954 cells with 3-day treatment of TBK1-II at 4 uM were used to compare with vehicle-treated controls. Microarray data was processed and normalized by lumi package from BioConductor in R with Quantile Method. Difference between the samples were calculated by Bayesian statistic using limma package from BioConductor in R to obtain Moderated T value for subsequent Pathway analysis.
Project description:Microarray analysis was performed at the UHN Microarray Centre (UHNMAC, Ontario, Canada) using Illumina HumanHT-12 v4 BeadChip with 500 ng of total RNA prepared by RNeasy mini kit (QIAGEN, Cat. No. 74104). Samples from HCC1954 cells with 3-day treatment of TBK1-II at 4 uM were used to compare with vehicle-treated controls. Microarray data was processed and normalized by lumi package from BioConductor in R with Quantile Method. Difference between the samples were calculated by Bayesian statistic using limma package from BioConductor in R to obtain Moderated T value for subsequent Pathway analysis. Total RNA extracted from HER2+ HCC1954 cells after 3 days treatment of TBK1-II inhibitor compared with vehicle control
Project description:MicroRNA-offset RNAs (moRs) were first identified in simple chordates and subsequently in mouse and human cells by deep sequencing of short RNAs. MoRs are derived from sequences located immediately adjacent to microRNAs (miRs) in the primary miR (pri-miR). Currently moRs are considered to be simply a by-product of miR biosynthesis that lack biological activity. Here we show for the first time that a moR is biologically active. We now demonstrate that endogenous and over-expressed moR-21 significantly alters gene expression and inhibits the proliferation of vascular smooth muscle cells (VSMC). We report that the seed region of moR-21 as well as the seed match region in the target gene 3'UTR are indispensable for moR-21-mediated gene down-regulation. We further demonstrated that moR-21-mediated gene repression is Argonaute 2 (Ago2) dependent. In addition, we find that miR-21 and moR-21 may regulate different genes in a given pathway and can oppose each other in regulating certain genes. Taken together, these findings provide the first evidence that microRNA offset RNA regulates gene expression and is biologically active. Primary mouse aortic smooth muscle cells (AoSMCs) were transfected with scrambled control or moR-21 mimetics at 5nM final concentration. Triplicate samples were prepared for each treatment. Total RNA was isolated at 48hr post-transfection. Labeling and hybridization to MouseRef-8 v2.0 Expression BeadChip (llumina) were performed according to the Yale Center for Genome Analysis protocol (YCGA, http://ycga.yale.edu/). Beadstudio suite of programs were used to calculate the quantile normalized expression values for probe sets. Bioconductor packages Lumi and Limma Linear models and empirical Bayes methods for assessing differential expression in microarray experiments were use to process and annotate the expression values and calculate the fold changes and P-values.