Project description:Microarray technology permits high throughput comparisons of gene expression in different parasite stages or sexes. We now report the first use of this technology for analysis of gene expression in filarial worms. The slide array (comprised of 65 mer oligos representing 3569 EST clusters) was spotted with sequences selected from the extensive Brugia malayi EST database (http://nema.cap.ed.ac.uk/nematodeESTs/nembase.html#Annotation). Arrays were hybridized with male and female cDNA and developed with Cy5- and Cy3-fluorescent 3DNA capture reagents. The experimental design included both biological and technical (dye-flip) replicates.
Project description:We classified samples and deciphered a key genes signature of intratumor heterogeneity by Principal Component Analysis and Weighted Gene Co-expression Network Analysis. At the genome level, we identified common GB copy number alterations and but a strong inter-individual molecular heterogeneity.
Project description:Using RNA sequencing, we produced a spatiotemporal transcriptome based on 65 samples. Then, we constructed a weighted gene co-expression network of these three Vitis species and defined 17 modules which were correlated to anthocyanins concentrations, developmental stages and species.
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: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:Mitochondrial DNA encodes thirteen subunits of the oxidative phosphorylation (OXPHOS) system, which are synthesized inside the organelle and essential for cellular energy supply. How mitochondrial gene expression is regulated and integrated into cellular physiology is little understood. Here, we performed a high-throughput screen combining fluorescent-labelling of mitochondrial translation products with siRNA-mediated knockdown, to identify cellular kinases regulating translation. As proof of principle, the screen identified known kinases that affect mitochondrial translation, and it also revealed several kinases not yet linked to this process. Among the latter, we focused on the primarily cytosolic kinase FN3K, which localizes partially to mitochondria, to support translation. Mass spectrometric (MS) bottom-up analysis of peptide samples after FN3K-flag immunoisolation in isolated mitochondria (transfected with FN3K-flag plasmid) enabled the identification of several proteins of the mitochondrial ribosome to be interacting with FN3K. Further experiments showed that FN3K likely modulates the assembly of mitochondrial ribosomes, thereby affecting translation. Overall, our work provides a reliable approach to identify new protein functions for mitochondrial gene expression, in a high throughput manner.
Project description:The aim was to examine changes in gene expression of the endometrium exposed to long-term tamoxifen treatment in comparison to age matched controls. To achieve this, endometrial tissues were obtained from women receiving tamoxifen treatment who were undergoing a hysterectomy. Using cDNA microarrays, gene expression changes in the postmenopausal endometrium of these women was compared with that in endometrium of age matched women not receiving tamoxifen. Endometrial tissue from post-menopausal women was obtained following ethical approval from the Leicester NHS Trust. None of the women had received any hormonal treatment for two months prior to the procurement of the specimens. Tissues were taken from untreated women (n=6) or those treated for 4 to 5 years with tamoxifen (20mg/day) (n=4), aged 58-82 (65 ± 9.1, mean ± SD). Total RNA was extracted. Controls were pooled. RNA labelling, hybridisation and analysis of fluorescence was carried out as described by Turton et al (2001). Cy3/Cy5 Dye swap labelling was carried out on samples from each patient. Reference: Turton NJ et. al. (Oncogene (2001) 20, 1300-1306
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:This SuperSeries is composed of the following subset Series: GSE27331: Gain of the oncostatin M receptor in cervical squamous cell carcinoma is associated with adverse clinical outcome [penn1Mb data] GSE27332: Gain of the oncostatin M receptor in cervical squamous cell carcinoma is associated with adverse clinical outcome [camb1Mb data] GSE27673: An integrated genomics approach for novel biomarker discovery in squamous cell cervical carcinoma Refer to individual Series
Project description:Using integrated proteomic and RNA sequencing analysis of COPD and control lung tissues, we identified molecular signatures in COPD.