ABSTRACT: Dataset contains mixture of 41 standards mixed at equimolar concentration of 10uM in Fecal background and then subsequently diluted down to 100 pM. Each sample ran in triplicate.
INSTRUMENT(S): TSQ Quantum Access, Q Exactive
ORGANISM(S): Standard Homo Sapiens (ncbitaxon:9606)
Project description:Dataset contains mixture of 41 standards mixed at equimolar concentration of 10uM and then subsequently diluted down to 100 pM. Each sample ran in triplicate.
Project description:CCE mESCs were transfected with either empty pCAGGS vector or HA-MEK5DD (S311D T315D) construct for 48 hours. 24 hours prior to lysis, mESCs were either treated with 10uM AX15836 or DMSO control, and transfected mESCs selected with puromycin. Conditions were performed in triplicate.
Project description:Peritoneal metastasis (PM) is associated with a poor prognosis in patients with colorectal cancer (CRC) or appendiceal adenocarcinoma (AA). Detection of PM remains challenging due to the low sensitivity of current imaging modalities and the invasiveness of tissue pathology-based diagnostics. Here, we demonstrate for the first time the feasibility of using 5-hydroxymethylcytosine (5hmC) signatures derived from circulating cell-free DNA (cfDNA) as minimally biomarker s for PM. Using nano-hmC-Seal on plasma-derived cfDNA and next-generation sequencing, we obtained genome-wide 5hmC profiles from 112 CRC or AA patients (n = 71 PM+ and n = 41 PM–) and 73 non-cancer controls. Predictive models trained on genomic region 5hmC levels distinguished PM status with an area under the curve of 0.827 (92.4% sensitivity, 46.1% specificity). Pathway enrichment analysis identified epigenetically dysregulated cancer, cell migration, adhesion and immune-related pathways in PM. This study lays a foundation for future clinical assay development for PM.
Project description:Dataset contains 137 Standards mixed together at equimolar concentration of 10uM. Subsequent 1:10 dilutions down to 100pM are made. Sequence of all samples injected 3 times on different days under the identical conditions
Project description:Gender dependent gene expression in the kidney of 36 day old rats using the Affymetrix GeneChip rat expression set 230 array RAE230A. mixed model ANOVA using log2 transformed signal intensity of PM. Keywords: repeat
Project description:Open tenotomy of the Achilles tendon of 6 rats was performed. The animals were divided into two groups according to exposure of PM2.5 (particulate matter less than 2.5 µm): control group (Non-PM group) or PM exposure group (PM group). After 6 weeks of PM exposure, the tendon DNA was extracted and anlyzed. Genome-wide DNA methylation profiles were determinen. DNA amplicons were prepared using Differential Methylation Hybridization (DMH) method, subsequently hybridized on to the Customized Agilent Rat CpG island Microarray. The goal was to unravel the DNA methylation patterns in different subgropus of tendon tissue according to partciulate matter exposure.
Project description:To study the effects of Notch signal in tumor associated endothelial cells ,we conducted a RNA sequence assay. Briefly, TECs were isolatedas described above from LLC tumors 14 days after inoculation in 3 pairs of NICeCA and control mice. Total RNA was extracted using Trizol, and RNA integrity was evaluated using the Agilent 2200 Tape Station (Agilent Technologies, Santa Clara, California, USA) and each sample had the RINe above 7.0. rRNA was removed using the EpicentreRibo-Zero rRNARemoval Kit ( Illumina, San Diego, CA). Remaining RNA was fragmented into approximately 200bp fragments. Subsequently, the sample was subjected to first and second strand cDNA synthesis followed by adaptor ligation and enrichment with a low-cycle PCR usingTruSeq® RNA LT/HT Sample Prep Kit (Illumina). The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit®2.0 (Life Technologies) and then diluted to 10 pM for cluster generation in situ on the HiSeq3000 pair-end flow cell followed by sequencing (2×150 bp) on HiSeq 3000.
Project description:Exposure to ambient airborne particulate matter (PM) has been associated with almost 9 million premature deaths per year worldwide. Ports are essential infrastructure for trade and transport, with over 80% of the world’s international trade volume travelling by sea, yet there is little understanding of the potential health effects of PM from ships. Here, we studied the elemental and toxicological characteristics of size-fractionated PM collected at different areas of a busy European mixed-use port. We found that unregulated ultrafine PM, a PM size fraction <100 nm in aerodynamic diameter, originating from a cruise-ship source, was highly enriched compared to ultrafine PM from other sites in tracers of heavy fuel oil combustion (V and Ni), with Co identified as a novel tracer. In cell models of airway and alveolar epithelium, this cruise ship-associated ultrafine PM was markedly more pro-inflammatory than PM from other sites, while simultaneously reducing expression of a range of genes associated with the innate antiviral response. Investigation of the effects of the three metals found to be enriched in our cruise-ship ultrafine PM showed that these effects could be reproduced by vanadium exposure, which reduced interferon signalling and increased permissiveness to viral infection, facilitating replication of the respiratory viruses rhinovirus-16 and SARS-CoV-2. Our findings suggest that, despite a series of regulations introduced over the last 20 years, cruise ship-associated emissions of PM from heavy fuel oil combustion may exert disproportionate effects on health compared to PM from other sources. In particular, the effects manifest themselves through induction of a response with characteristics of a poor viral infection prognosis. More broadly, current regulations, which neglect PM source- and composition-related variations, and ultrafine PM in general, may need strengthening to better mitigate health effects resulting from exposure to PM.
Project description:We investigated whether mouse serum autoantibody binding patterns on random-sequence peptide microarrays (immunosignaturing) can be used for diagnosing and predicting the onset of lupus and its central nervous system (CNS) manifestations. Submitter states "We have no processed data to submit. We have no gpr files to submit." To identify possible predictive and diagnostic peptides of lupus and CNS-lupus, we carried out two studies and selected peptides in common across both studies. In the first study we tested 3-6 MRL/lpr, MRL/mp and C3H/HeJ mice at four months of age. For study two we tested 9-10 MRL/lpr and MRL/mp at 1.5 and 4 months of age. In both studies the mice sera were diluted 1/500 and analyzed using microarray peptides from platform GPL14921. We ran each sample in triplicate. The MRL/lpr and MRL/mp are the autoimmune strains and the C3H/HeJ is the control strain.