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:Background: Previous array CGH analyses have revealed several recurring genomic alterations in urothelial carcinoma. The most common genomic amplifications occur at 6p22 and 1q21-24. The main target gene at 6p22 is believed to be E2F3. This gene is frequently co-amplified with CDKAL1 and SOX4 and there are reports on 6p22 amplifications that do not include the E2F3 locus. Previous array CGH analyses have indicated multiple possible target regions at 1q21-24. However, due to complex rearrangements it has been difficult to identify specific 1q21-24 target regions and target genes. Results: We show that the most commonly amplified gene at 6p22 is SOX4 and that SOX4 can be amplified and over expressed without E2F3 or CDKAL1 being included in the amplicon. Hence, our data point to SOX4 as an auxiliary amplification target at 6p22. We further show that at least three amplified regions are observed at 1q21-24. Copy number data, combined with gene expression data, highlighted BCL9 and CHD1L as possible targets in the most proximal region and MCL1, SETDB1, and HIF1B as targets in the middle region, whereas no obvious gene targets could be determined in the most distal amplicon. We also highlight the enrichment of G4 quadruplex sequence motifs and the high number of intraregional sequence duplications, both known to contribute to genomic instability, as prominent features of the 1q21-24 region. Conclusions: Our detailed analyses of the 6p22 amplicon in urothelial carcinomas suggest SOX4 as an auxiliary target gene for amplification. We further demonstrate three separate target regions for amplification at 1q21-24 and identified BCL9, CHD1L, MCL1, SETDB1, and HIF1B as likely target genes within these regions. The study was conducted on genomic DNA from 68 primary fresh-frozen urothelial carcinoma tumors analysed using a Agilent SurePrint G3 4x180k Custom CGH Microarray Platform (028432). Samples were selected based on the presence of copy number alterations observed on lower resolution genomic data (32K BAC array). The majority of the BAC data is publicly available in GEO submissions GSE32535 and GSE19915. CN profiles for a minority of samples were derived from Illumina Methylation27k arrays according to Lauss et al 2012 [PMID: 22705924] and can be recreated from the data deposited in GSE33510 (derived CN data). Sample names are the same between all studies. This dataset also partly overlaps with Series GSE32894 (gene expression data). Names of the overlapping sample names are the same and indicated in the description field. Data from GSE32894 was used to calculate correlations between CN and gene expression.
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:This study investigates the proteomic alterations in striatal synaptic mitochondria isolated from 3-month-old wild-type and Pink1 KO rats using the SWATH-MS strategy. This dataset consists of 32 raw MS files, comprising 8 DIA (SWATH) and 24 DDA runs on a TripleTOF 5600 (SCIEX). Our findings revealed synaptic mitochondrial proteomic changes due to loss of Pink1.
Project description:The purpose of this experiment was to generate an additional RNAseq dataset of human cardiomyocytes exposed to doxorubicin for 24 hours. For robustness 7 biological replicas were generated per exposure group.
Project description:Quantitative proteomic analysis of undiluted human vitreous biopsies collected at the time of primary surgical repair of rhegmatogenous retinal detachment (RRD), comparing patients who later developed proliferative vitreoretinopathy (PVR; n=8) with matched RRD controls who did not (n=8). Vitreous samples were processed by S-Trap digestion, labeled with TMT 10-plex reagents, and analyzed by LC–MS/MS on a Thermo Q Exactive instrument (two TMT 10-plex sets, two LC-MS/MS injection replicates per set; four .raw files total). Identification and quantitation were performed using Mascot followed by the proteoQ R pipeline. The dataset comprises 879 quantified proteins after stringent contaminant filtering. The deposition is intended as a methodologically transparent reference dataset of the baseline RRD vitreous proteome for future meta-analyses.
Project description:The purpose of this experiment was to generate an RNAseq dataset of human cardiomyocytes with lower levels of FOXO3 exposed to doxorubicin for 24 hours. Stable knock-down of FOXO3 was achieved using lentiviral shRNA construct. As negative control cells bearing an shRNA targeting GFP was used
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:Temporally restricted feeding is known to impact the circadian clock. This dataset shows the effects of temporally restricted feeding on the hepatic transcriptome. C57/B6 mice were entrained for two weeks to a temporally restricted feeding schedule. Food was made available only between ZT(CT)1 and ZT(CT)9. Mice were then released into constant darkness while food availability was still restricted and liver tissue was collected at the indicated timepoints on the second day in constant darkness. Total RNA was extracted and 5ug were submitted to the standard Affymetrix protocol for amplification, labeling and hybridization.
Project description:Temporally restricted feeding has a profound effect on the hepatic circadian clock. While the circadian clock is largely unaffected by by extensive fasting, many transcripts are known to be affected by a fasting paradigm. This dataset shows the effect of extensive fasting on dynamic gene expression in the liver C57/B6 mice were entrained to ad libitum feeding schedule for two weeks. They were then released into constant were food was withdrawn at CT16. On the second day in constant darkness tissue was collected at the indicated timepoints. Total RNA was extracted and 5ug of total RNA was used for the standard Affymetrix protocol of amplification, labeling and hybridization