Project description:Vascular cell types are under-represented in standard single-nucleus RNA-Seq studies of human frozen post-mortem brain tissue. Using a novel microvessel-enrichment procedure allows to obtain highly purified fractions of vascular cell types and their corresponding parenchymal fraction of the same post-mortem brain tissue sample.
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: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: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: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: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:Sample tissue: peripheral blood Disease: normal subject, patients with type 2 diabetes (diabetic nephropathy +, -) Samples for gene expression analysis were obtained before and after the event. Keywords: equivalent probe, disease response
Project description:Arabidopsis plants, ecotype Columbia, were sprayed with surfactant alone (0.01% Silwet) or surfactant and 1mM salicylic acid until all leaves were wet, 3 to 4 weeks after germination (before flowering). Leaves were harvested and frozen in liquid nitrogen. Three biological replicates were obtained over a period of 6 months. For each replicate, RNA was extracted using standard phenol/chloroform protocol and biotin-labeled cRNA was synthesized. cRNA was hybridized to 6 ATH1 GeneChip arrays. Cel files produced by the Affymetrix software were imported into R. Background subtraction, normalization and probe summaries were performed with the rma, quantile.normalization and median polish options of the rma function. Comparison of the SA- versus mock-treated tissue provides insight on the genes involved in systemic acquired resistance in Arabidopsis. Keywords: salicylic acid, Arabidopsis, stress response, defense,