Project description:SNP array data from 127 hepatocellular adenomas and carcinomas were used to detect recurrent copy number alterations. 48 tumors were analyzed with Illumina HumanCNV370-Duo v1.0 chips. 79 tumors were analyzed with Illumina HumanOmniExpress BeadChip.
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:cea06-01_uranyl_nitrate - time course uranyl nitrate response - Dynamic analyses of transcriptomic response to urany l nitrate - Plants are grown on sand and transfert in hydroponic culture during 2 days and then expose or not to 50uM uranyl nitrate at pH 4.5 in water or only to water at pH 4.5. Roots and leaves were collected independently after 2h, 6h and 30h of treament. Keywords: organ comparison,time course,treated vs untreated comparison 20 dye-swap - CATMA arrays
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:This dataset comprises a Tandem Mass Tag (TMT)-based quantitative proteomic analysis of serum samples from patients with postherpetic neuralgia (PHN) compared to healthy control subjects. The study aimed to identify differentially expressed proteins involved in the pathogenesis of neuropathic pain. Peripheral blood serum was collected from three PHN patients and three age- and sex-matched healthy volunteers. Proteins were digested with trypsin, labeled with TMT isobaric tags, and fractionated by reversed-phase liquid chromatography. The peptides were analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) on a SCIEX TripleTOF 5600+ instrument. Our analysis identified 127 differentially expressed proteins (79 down-regulated and 48 up-regulated in the PHN group). Notably, Endoglin (CD105), a key endothelial cell membrane glycoprotein, was one of the significantly down-regulated proteins. This discovery was subsequently validated by ELISA in a larger cohort (n=30 per group). The proteomic profiling presented in this dataset led to the mechanistic hypothesis that reduced Endoglin expression contributes to neuropathic pain by disrupting the blood-spinal cord barrier (BSCB) integrity via inhibition of the TGF-β/Smad2 signaling pathway. This hypothesis was successfully confirmed in a spared nerve injury (SNI) rat model through behavioral, biochemical, and histological experiments, as detailed in our associated manuscript. This dataset provides the foundational proteomic evidence for the role of Endoglin in neuropathic pain and serves as a valuable resource for identifying potential biomarkers and therapeutic targets.
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
Project description:Expression data derived from this analysis was used to compare expression signatures between genomic subgroups identified from DNA copy number analysis. In this dataset, we include the expression data obtained from 79 stage Ta primary bladder tumours
Project description:Genome wide DNA methylation profiles of human Liver tissue. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 485,000 CpGs. Dataset includes 79 samples from Germany. The goal of the study was to evalute the relationship between body mass index and DNA methylation levels. Bisulphite converted DNA from the 79 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip.