Transcription profiling of human MCF10A-Myc breast cancer cell line treated with dexamethazone or an ethanol control, sampled at 4 timepoints
ABSTRACT: This series contain time course microarray data from MCF10A-Myc cells treated with either ethanol or Dexamethasone for 30 min, 2 hr, 4 hr, and 24 hr. This series contains three biological replicates that were analyzed as independent replicate experiments (data were normalized within each replicate experiment, not across all samples). Keywords: time course MCF10A-Myc cells were subjected to 72 hrs of growth factor withdrawal followed by treatment with either vehicle (ethanol) or Dex (10-6 M) for 0.5, 2, 4 or 24 hrs. Total RNA from each sample was extracted using Qiagen’s RNeasy Kit. Preparation of biotinylated cRNA and hybridization to oligonucleotide arrays (Affymetrix human genome genechip HG-U133A) were performed at the University of Chicago Microarray Core Facility. HG-U133A genechip contains 22,215 probe sets that represent approximately 16,000 human genes. The complete procedure was repeated independently three times. Gene chips were scanned and analyzed using Robust Multi-array Average (RMA) algorithm.
Activation of the glucocorticoid receptor (GR) plays a critical role in the stress response of virtually all cell types. Despite recent advances in large-scale genomic and proteomic data acquisition, identification of physiologically relevant molecular events downstream of nuclear hormone receptor activation remains challenging. By analyzing gene expression changes 30 min after dexamethasone (Dex) treatment, we previously found that immediate induction of serum and glucocorticoid-regulated kinas ...[more]
Project description:Given the heterogeneity of disease evident from study of the presentation, histomorphology, disease course, and molecular lesions of bladder cancer, a cohort of 8 non-muscle invasive and 11 muscle invasive bladder cancers were profiled for gene expression using the Affymetrix HG-U133A platform. Under an IRB-approved protocol, snap frozen tissues for 19 cases of bladder cancer were procured and profiled for gene expression using Affymetrix HG-U133A microarrays.
Project description:We sought to examine the mechanism through which phospho-mutants can contribute to the transformation of MCF10A acini. To investigate this, we examined the RNA abundance of Myc and Myc phospho-mutants (T58A, S71A/S81A, and Myc-4A) against a GFP control. Three independent biological replicates of the five samples (Myc, T58A, S71A/S81A, Myc-4A and GFP control) were isolated on day 4 and processed on Affymetrix HG-U133 Plus2 chips.
Project description:In the current study, we compared phosphoproteomic and proteomic changes in roots of different soybean seedlings of a salt-tolerant cultivar (Wenfeng07) and a salt-sensitive cultivar (Union85140) induced by salt stress. The root samples of Wenfeng07 and Union85140 at three-trifoliate stage were collected at 0 hr, 0.5 hr, 1 hr, 4 hrs, 12 hrs, 24 hrs and 48 hrs after been treated with 150 mM NaCl. LC-MS/MS based phosphoproteomic analysis of these samples identified a total of 2692 phosphoproteins and 5509 phosphorylation sites. Of these, 2344 phosphoproteins containing 3744 phosphorylation sites were quantitatively analyzed. Our results showed that 1163 phosphorylation sites were differentially phosphorylated in the two compared cultivars.
Project description:40 bladder cancer cell lines were profiled with their genome-wide gene expression patterns using Affymetrix HG-U133A chips. Experiment Overall Design: Total RNA sample of each of the 40 cell lines was obtained before the treatment of any anticancer compound.
Project description:Gene expression profiles during the differentiation of EPCs into OECs were analyzed. Experiment Overall Design: RNA was isolated from Human cord blood derived- EPC and differentiated OEC from EPC. HG-U133A 2.0 microarray (54675 human genes; Affymetrix Santa Clara, CA, USA) was performed.
Project description:This experiment contains manually annotated, systematically quality controlled and consistently nomalized human skeletal muscle gene expression data matrices of two platforms, total 1655 arrays: 1102 arrays from HG-U133plus2 and 553 arrays from HG-U133A . The dataset is a subset of a larger collection of 2852 arrays of 80 stuides from 20 platforms.