Project description:Fetal lung development is a complex biological process, which involves temporal and spatial regulations of many genes. To understand molecular mechanisms of this process, we investigated gene expression profiling of lungs at gestational day 18, 19, 20, 21, new born, and adult rats using in-house rat DNA microarray containing 6,000 known genes and 4,000 ESTs. 1,512 genes passed SAM test and 583 genes (402 known genes and 181 ESTs) had a 2-fold change at least at one time point. K-means cluster analysis revealed 7 major expression patterns. Furthermore, using GeneMapp, we identified 3 regulatory pathways: TGF beta signaling pathway, cell cycle, and G-protein signaling; and 2 metabolism pathways: proteasome degradation and glycolysis. Our results suggest a complex regulatory pathway for fetal lung development. Loop Design as following: D18-D19-D20-D21-NB-AD-D18
Project description:We report an integrated analysis incorporating DNA copy number analyses, somatic exon mutations, mRNA expression via RNA-sequencing, and shotgun mass spectrometry analysis of protein abundance in 108 surgically resected squamous cell lung cancers (SCC) with accompanying clinical outcome, evaluation of tumor pathology, and other clinically relevant data. We identified three major subtypes of SCC at the proteomic level, with two groups associated with inflammation/immune response or oxidation-reduction biology. Inflamed tumors could be further sub-classified based on neutrophil infiltration or antigen presentation proteomes and reflected patterns of infiltrating immune cells. No gene mutations, mRNA signatures, or proteomic subclasses were associated with outcomes; however, the presence of B-cell rich tertiary lymph node structures could be associated with better patient outcomes. By integrating our proteogenomic data with publicly available RNA interference screen data, we identified TP63, PSAT1, and AKR1C3 as vulnerabilities in SCC, particularly in the redox proteomic group. This cohort and its deep molecular data serves as an important resource to better understand biology and targets associated with SCC.
Project description:To identify substrates of the ubiquitinating E3 enzyme Rsp5 we applied purified Rsp5 to duplicate protein arrays. The Rsp proteins were expressed as fusion proteins to GST. We used as a control Ubr1, a RING domain containing E3 ligase We analyzed Rsp5 from S.cerevisiae on duplicate arrays, with four control chips, two without Rsp5 and two with Ubr1.
Project description:Cell line-based proteomics studies are susceptible to intrinsic biological variation that contributes to increasing false positive claims; most of the methods that follow these changes offer a limited understanding of the biological system. We applied a quantitative proteomic strategy (iTRAQ) to detect intrinsic protein variation across SH-SY5Y cell culture replicates. More than 95% of the quantified proteins presented a coefficient of variation (CV) <20% between biological replicates and the variable proteins, which included cytoskeleton, cytoplasmic and housekeeping proteins, are widely reported in proteomic studies. We recommend this approach as an additional quality control before starting any proteomic experiment.
Project description:Environmental stressors such as repeated social defeat may trigger powerful activation of sub-conscious parts of the brain. We examine the consequences of such stress in male rats on the pituitary gland. We prepared 20 Sprague Dawley rats. 10 of them were exposed to stress induced by the resident-intruder paradigm while the other 10 were controls. After dislocation of the neck under isoflurane anaesthesia, the pituitary gland was harvested. Total RNA was isolated from the tissues and used in mRNA sequencing.
Project description:This SuperSeries is composed of the following subset Series: GSE24037: Salivary cytokine alterations in HIV infection part 1 GSE24064: Salivary cytokine alterations in HIV infection part 2 Refer to individual Series
Project description:Pseudomonas plecoglossicida is a facultative pathogen that is associated with diseases of multiple fish, mainly at 15-20 °C. Although fish disease caused by P. plecoglossicida has led to significant economic losses, the mechanisms of the temperature-dependent virulence are unclear. Here, we try to identify potential pathogenicity mechanisms and demonstrate the direct regulation of virulence factors by temperature with iTRAQ.