Project description:miRNAs were extracted from plasma samples of healthy volunteers, patients with Barrett’s esophagus and patients with esophageal adenocarcinoma. We used the Serum / Plasma Focus miRNA PCR panel (Exiqon, Denmark) to quantitate miRNA presence in the different patient groups.
Project description:Sewage samples were collected and concentrated for Human and animal viruses. Viruses were cultured on Buffalo Green Monkey Cells (BGMK) and their genomic DNA/RNA were extracted and labeled with Cy3 and Cy5 respectively. Labeled DNA/RNA were hybridized unto the array and signals generated were analyzed to indicate the presence of target viruses. Keywords: Detection of pathogens within environmental sample (Viruses)
Project description:Kunming mice were total body irradiated by 0.5Gy and 2Gy carbon ions radaition. After 24 hours, blood was collected and serum was isolated. Total RNA of serum sample was extracted by miRNeasy Serum/Plasma Kit (Qiagen, Germany). Then, miRCURY LNA™ Universal RT microRNA PCR, Ready-to-Use Mouse&Rat Panel I V3 (Exiqon, Denmark) containing 384 assays was performed to profile miRNAs differential expression in these serum sample.
Project description:To identify tumor compartment-specific microRNA expression in stage I non-small cell lung cancer in humans, surgically resected and formalin-fixed tumor tissues were used in laser capture microdissection to isolate tumor epithelia and stroma. Total RNA extracted from the microdissectates was analyzed for microRNA expression using the 7th generation miRCURY™ locked nucleic acid microarray platform (Exiqon®, Vedbaek, Denmark).
2014-12-31 | GSE42425 | GEO
Project description:Environmental samples collected from Mariana Trench
Project description:Total RNA was extracted from V. angularium susceptible and resistant rainbow trout, tissues (liver, spleen, gill), in different time points using GenEluteTM mammalian RNA kit (RTN350, Sigma-Aldrich, Denmark). After measuring quantity (NanoDrop 2000 spectrophotometer (Saveen & Werner, Denmark)) and quality (gel electrophoresis) of RNA, cDNA was synthetised in T100 thermocycler, Biorad, Denmark, using Oligo d(T)16 primer and TaqMan® Reverse Transcription Reagents (cat.no. N8080234, Thermo Fischer Scientific, Denmark). Primers and probes for total of 28 genes including three housekeeping genes were synthesized at TAG Copenhagen AS, Denmark. qPCR reactions were run by Brilliant III Ultra-Fast QPCR Master Mix (600881, AH Diagnostics AS, Denmark) for all samples. The fold changes analysed by the simplified 2-ΔΔCq method. Fingerlings of rainbow trout (mean body weight of 12 g) were exposed (2 h bathing, 18°C) to the pathogen V. anguillarum serotype O1 in a solution of 1.5x107 cfu/ml and observed for 14 d. Disease signs appeared three days post exposure (dpe) whereafter morbidity progressed exponentially until 6 dpe reaching a total morbidity/mortality of 55% within 11 days. we sampled fish for immune gene expression analysis when they first showed clinical signs, fish without clinical signs at the same time point and finally fish surviving the exposure to the pathogen. The different immune gene expression profiles in the different groups were addressed when discussing possible resistance mechanisms in rainbow trout.
Project description:To understand the the effect of antagomir-17 treatment on human endothelial cells derived from human umbilical cord blood (UCB) CD34+ hematopoietic stem cells, we have employed mRNA sequencing. The antagomiR-17 used in this study was purchased from Dharmacon and cell transfection was performed using Lipofectamine RNAiMAx from Life Technologies. Scramble antagomiR from Ambion was used as control. Cells were transfected with antagomiR-17 or scrambled antagomiR for 48 hours. After 48 h, the cells were collected, RNA was isolated and RNA samples were shipped to Exiqon Services, Denmark for mRNA sequencing. All sequencing experiments (RNA integrity measurements, library preparation and next generation sequencing) were conducted at Exiqon Services, Denmark.
Project description:Tracheal aspirate (TAs) samples were collected from intubated preterm infants with hemodynamically significant intracardiac shunt (ICS), and a diagnosis of ICS-BPD/ICS-BPD-PH. 36 TA samples were analyzed. Small RNAs were extracted and the expression miRNAs was detected with PCR arrays.
Project description:In this study, we analyzed the role of miR-21 in liver regeneration after partial hepatectomy (PHx) in chronic ethanol-treated rats. Male Sprague-Dawley rats were fed a liquid diet containing 36% of total calories derived from ethanol for 5 weeks; corresponding pair-fed calorie-matched controls were fed diets in which ethanol calories were replaced by carbohydrate. After 5 weeks, locked nucleic acid (LNA)-modified oligo antisense to miR-21 (AM21, Exiqon, Vedbaek, Denmark) was used to inhibit miRNA in vivo, and rats were subjected to 70% PHx. Liver samples were collected at 24h after the surgery. The excised liver samples at t=0 served as within-animal controls. Rat Gene 2.0 ST (Affymetrix, Santa Clara, CA) arrays were used to obtain global gene expression data from pooled liver samples (pools of 3 or 4 biological replicates/array, total 8 arrays).
Project description:To investigate the mechanism of annual rhythms in Japanese cedar, annual time series samples were collected from the cuttings planted in natural condition. Also, to investigate the effects of photoperiod and temperature during transition to dormancy, the samples of cuttings grown in the controlled-environmental chamber were analyzed by a microarray.