Project description:The annotation of the Affymetrix HTA 2.0 array was updated to optimise the detection of both coding and non-coding RNA in human skeletal muscle biopsy samples by removing invalid and low signal-high-variance probes. A transcript level CDF specific to skeletal muscle is provided to use within the standard aroma.affymetrix pipeline.
Project description:Comparison of Gene Expression in Uterine Smooth Muscle Tumors (including normal myometrium, benign uterine leiomyoma, malignant uterine and extra-uterine leiomyosarcoma. Total RNA was isolated with Trizol and converted to labeled cRNA by standard Affymetrix protocols. Before analysis, Avg Diff values were normalized to a sum of 3 million for each probe set on the chip and values less than 20 were adjusted to 20 to allow log scaling in subsequent analysis. Keywords: other
Project description:Clinical specimens were collected from patients with Acute Lymphoblastic Leukemia (ALL) and from non-leukemic controls. Total RNA (including small RNA) was profiled using the Affymetrix GeneChip miRNA 4.0 array to identify differentially expressed miRNAs between ALL and controls Raw CEL files were generated using standard Affymetrix GeneChip scanning and feature extraction (AGCC or equivalent). Expression values were obtained in R using RMA normalization, followed by probe filtering was applied. Differential expression was assessed with limma using an ALL vs CTRL contrast with Benjamini–Hochberg FDR correction.
Project description:Forty male C57BL6 mice 12-15 weeks old fed chow ad libitum. 30 mice underwent adrenalectomy (Adx) and 10 others a sham-Adx. Three or 24h before tissue sampling, groups of 10 mice received an I.P. injection of cortisol (0.1 mg per mice), while the remaining Adx and intact mice received an I.P. injection of the vehicle (ethanol) 24 h prior to the sacrifice. All mice were killed within a period of a few hours. Gastrocnemius muscle were dissected and pooled together for each one of the four groups. Total RNA was isolated by Trizol. Samples were processed following the labeling protocol from Affymetrix. In the MG-U74A2, each of the 12488 murine transcripts are represented by 16 probe pairs of 25mer. Images were scanned using a GeneChip scanner 3000 with autoloader, and analyzed with the MAS 5.0 software (Affymetrix). The ratio of fluorescence intensities for the 5' end and the 3' end of beta-actin and glyceraldehyde 3-phosphate dehydrogenase was less than 2. This microarray analysis was performed once. Keywords = Skeletal muscle Keywords = gastrocnemius Keywords = adrenalectomy Keywords = glucocorticoids Keywords: other
Project description:Female Ames dwarf mouse (df/df) with ad libitum access to water and standard pelleted food (LabDiet, PMI Feeds, Inc., St Louis, MO) caged with microisolator filter tops. Mice were killed between 24 to 26 months of age, tissues removed, rapidly frozen on dry ice, and stored in liquid nitrogen. Total liver RNA was isolated from frozen tissue as described (T. Tsuchiya, J.M. Dhahbi, X. Cui, P.L. Mote, A. Bartke, S.R. Spindler, Physiological Genomics, Submitted). mRNA levels were measured using the Affymetrix mouse U74Av2 array according to standard protocols. After hybridization, arrays were scanned using a Hewlett-Packard GeneArray Scanner. Image analysis was performed as described (Cao SX, Dhahbi JM, Mote PL, and Spindler SR. Genomic profiling of short- and long-term caloric restriction effects in the liver of aging mice. Proc Natl Acad Sci U S A 98: 10630-10635, 2001). A more detailed description of the methods can be found in (T. Tsuchiya, J.M. Dhahbi, X. Cui, P.L. Mote, A. Bartke, S.R. Spindler, Physiological Genomics, Submitted). Keywords = Ames dwarf Keywords = mouse Keywords = Affymetrix Keywords = caloric restriction Keywords: parallel sample
Project description:Female Ames dwarf mouse (+/+ or +/df) with ad libitum access to water and standard pelleted food (LabDiet, PMI Feeds, Inc., St Louis, MO) caged with microisolator filter tops. Mice were killed between 24 to 26 months of age, tissues removed, rapidly frozen on dry ice, and stored in liquid nitrogen. Total liver RNA was isolated from frozen tissue as described (T. Tsuchiya, J.M. Dhahbi, X. Cui, P.L. Mote, A. Bartke, S.R. Spindler, Physiological Genomics, Submitted). mRNA levels were measured using the Affymetrix mouse U74Av2 array according to standard protocols. After hybridization, arrays were scanned using a Hewlett-Packard GeneArray Scanner. Image analysis was performed as described (Cao SX, Dhahbi JM, Mote PL, and Spindler SR. Genomic profiling of short- and long-term caloric restriction effects in the liver of aging mice. Proc Natl Acad Sci U S A 98: 10630-10635, 2001). A more detailed description of the methods can be found in (T. Tsuchiya, J.M. Dhahbi, X. Cui, P.L. Mote, A. Bartke, S.R. Spindler, Physiological Genomics, Submitted). Keywords = Ames dwarf Keywords = mouse Keywords = Affymetrix Keywords = caloric restriction Keywords: parallel sample
Project description:The requirement of frozen tissues for microarray experiments limits the clinical usage of genome-wide expression profiling using microarray technology. Keywords: Lung Cancer Prognosis, Gene Expression Signature, Formalin Fixed Paraffin Embedded Samples The goal of this study is to test the feasibility of developing lung cancer prognosis gene signatures using genome-wide expression profiling of formalin-fixed paraffin-embedded (FFPE) samples, which are widely available and provide a valuable rich source for studying the association of molecular changes in cancer and associated clinical outcomes. FFPE tumor specimens were collected, and total RNA was processed for analysis on the Affymetrix U133 plus 2.0 arrays according to Affymetrix protocols. The quality control procedure for microarray data analysis was based on the percentage of present calls calculated by the MAS5 package. We selected 55 arrays with at least 15% of probe sets present, and we selected 1400 probe sets that present on all 55 arrays for data analysis. After microarray analysis QC, we used the RMA background correction algorithm to remove non-specific background noise. A robust regression model was fitted to the probe level data, and the fitted expression values for the probes at the 3' end were used to summarize the probe set expression values. Quantile-quantile normalization was used to normalize all the arrays. The 55 samples and the derived gene expression values for 1400 genes based on the robust regression model were used to develop gene signatures and were uploaded as supplementary data (GSE29013_fitted_1400_probes.txt).