ABSTRACT: 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: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.
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:Exposure to ambient particulate matter (PM) is associated with adverse health effects. Yet, due to the complexity of its chemical composition, the molecular effects of PM exposure and the mechanism of PM-mediated toxicity remain largely unknown. Here, we show that water-soluble inorganics such as nitrate and sulfate ions, rather than PM themselves, are responsible for perturbing gene expression in the lungs by rapidly penetrating the lung surfactant barrier to the alveolar region. Furthermore, from high-throughput sequencing of lung adenocarcinoma cells, we find that exposure to nitrate and sulfate ions activates the cholesterol biosynthetic metabolism and induces the expression of genes related to tumorigenesis and inflammatory response, particularly interferon-gamma. Transcriptome analysis of mouse lungs exposed to nitrate/sulfate aerosols further supports our findings. Notably, we find that exposure to nitrate/sulfate mixture leads to a unique gene expression pattern that is not observed when nitrate or sulfate is treated alone. Our work suggests the water-soluble ions as a potential source of PM-mediated toxicity and provides a roadmap to unveil the working mechanism of health hazards of PM exposure.
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:We report the development of an RNA sequencing method – AQRNA-seq – that minimizes biases and enables absolute quantification of all small RNA species in a sample mixture. Validation of AQRNA-seq library preparation and data mining algorithms using a 963-member microRNA reference library, RNA oligonucleotide standards of varying lengths, and northern blots demonstrated a direct, linear correlation between sequencing read count and RNA abundance.
Project description:This MassIVE dataset contains the standard compounds used to verify Level 1 annotations for the Metabolomics Annotation Collaboration. It contains two folders, which are labeled with the instrument (Orbi), the polarity [Positive (POS)], and the file type (Raw or mzML). Each folder contains 42 files: the extraction blanks (EXBLANK), Methanol/waste blanks (Wasteblank), the botanical of interest, Withania somnifera (WS03), a 10 uM mixture of 10 standards (WSSTDMix_10uM), and 10 individual standards (STD01-STD10), each in triplicate (ABC or 123).
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.