Project description:The objective is to generate a robust and validated predictor profile for chemotherapy response in patients with mCRC using microarray gene expression profiles of primary colorectal cancer tissue. To define a gene signature of response to chemotherapy in metastatic colorectal cancer, samples were obtained from 40 patients from Marques de Valdecilla Hospital who underwent primary surgery. Gene expression was detected and quantified using the Human Whole Genome U133 Plus 2.0 array (Affymetrix), containing 54675 human gene probes. The validation set consisted of 119 samples from Hospital Virgen del Rocio, Seville, Spain; Hospital Virgen de la Victoria, Malaga, Spain; Hospital de la Merced, Osuna, Spain and Hospital MarquM-CM-)s de Valdecilla, Santander, Spain, and included 86 tumor samples (40 coming from the training set and 46 from newly treated CRC patients) and 33 normal tissue samples of CRC patients used as controls. Custom-designed TaqManM-BM-. Low Density Arrays (TLDA) 7900 HT Micro Fluidic Cards including the 161 genes selected for validation were run and analyzed by the ABI PRISMM-BM-. 7900HT Sequence Detection System (SDS 2.2, Applied Biosystems) according to manufacturer's protocol (Applied Biosystems). Expression of target miRNAs was normalized in relation to the expression of GAPDH. Cycle threshold (Ct) values were calculated using the SDS software v.4.2 using automatic baseline settings and a threshold of 0.2. Relative quantification of gene expression was calculated by the 2M-bM-^HM-^RM-NM-^TCt method (Applied Biosystems user bulletin no. 2 (P/N 4303859)). This submission represents the RT-PCR component of the study only
Project description:The objective is to obtain miRNA representative signatures both in plasma and bronchoalveolar cell fraction that could serve as biomarker in respiratory diseases. The identification of new less invasive biomarkers is necessary to improve the detection and prognostic outcome of respiratory pathological processes. The measurement of miRNA expression through less invasive techniques such as plasma and serum have been suggested to analysis of several lung malignancies including lung cancer. These studies are assuming a common deregulated miRNA expression both in blood and lung tissue. The present study aimed to obtain miRNA representative signatures both in plasma and bronchoalveolar cell fraction that could serve as biomarker in respiratory diseases. we have compared circulating plasma miRNA with the bronchoalveolar cell fraction-derived miRNA patterns from 10 patients with several lung disease using a RT-qPCR assay.
Project description:The objective is to establish robust transcriptional regulation differences between squamous cell carcinoma (SCC) and adenocarcinoma (ADC) by studying miRNA and concurrent transcriptional profiles. This series represents the miRNA profiles only (not mRNA). The related mRNA data is in Series GSE42998. The present study was performed in 44 tumour samples following surgical resection for clinical early stage NSCLC (20 lung adenocarcinoma and 24 squamous cell lung cancer). Mature human miRNA expression was detected and quantified using the TaqMan® Low Density Arrays (TLDA). The Human MicroRNA Card Set v2.0 array is a two card set containing a total of 384 TaqMan® MicroRNA Assays per card to enable accurate quantification of 667 human microRNAs, all catalogued in the miRBase database.Expression of target miRNAs was normalized in relation to the expression of RNU48. Cycle threshold (Ct) values were calculated using the SDS software v.2.3 using automatic baseline settings and a threshold of 0.2. Relative quantification of miRNA expression was calculated by the 2−ΔCt method (Applied Biosystems user bulletin no. 2 (P/N 4303859)).
Project description:Cystic fibrosis (CF) is one of the commonest lethal genetic diseases in which the role of microRNAs (miRNAs) has yet to be explored. We hypothesized that unique miRNA expression profiles exist in CF versus non-CF bronchial epithelial cells so the our aim was to investigate whether unique miRNA expression profiles exist in CF, particularly in CF bronchial epithelial cells and explore their effects on influencing signaling pathways. The expression of 667 miRNAs were measured in bronchial brushings from individuals with and without cystic fibrosis (CFn=5, non-CF n=5). The 5 CF patient samples have been normalised to the controls so we get a final normalised value for 5 samples only. There are 2 raw data files for samples and controls as there are two cards A and B ran for each sample, for a total of 4 raw data files available on the Series record.
Project description:In this study, we performed a miRNA global profiling in human lung epithelial cells (A549) infected by two different subtypes of human influenza A viruses (H1N1 and H3N2). A549 cells were either mock-infected or infected at a multiplicity of infection (MOI) of 1 with H1N1 or H3N2 viruses, and total RNAs were isolated at 24 hours post-infection (hpi). An MOI of 1 was performed to ensure that 100% of the cells were infected at 24 hpi, a strategy that we have previously validated and used for a transcriptional profiling study of infected cells (Josset et al. , 2010). The purified RNAs were subjected to reverse transcription using a pool of miRNA RT primers (Human pool A v2.1, Applied Biosystems) and subsequently amplified and quantified by RT-qPCR in a TaqMan array MicroRNA card (Applied biosystems).
Project description:Previous epidemiological studies have shown that males tend to have an increased overall lifetime risk of developing atrial fibrillation (AF), whereas females tend to be more susceptible to the development of ventricular tachyarrhythmias resulting from long-QT syndrome and drug-induced Torsades de Pointes. In this study, we compared the transcript-level expression of 89 ion channel subunits, calcium handling proteins, and other transcription factors in the left atria (LA) and ventricles (LV) of human hearts of both genders. Total RNA from the LA and LV of failing male (n=9), failing female (n=7), nonfailing male (n=9), and nonfailing female (n=9) hearts was probed using a custom-designed Taqman gene array from Applied Biosystems. Tissues from LA (n=22), LV (n=22), LV endocardium (n=12), and LV epicardium (n=12) were analyzed by the Applied Biosystems SDS 2.3 software using the threshold cycle (Ct) relative quantification method with GAPDH as an endogenous control.
Project description:Newborn Balb/c mice were injected with 1.5x10^6 fluorescent-forming units (ffu) of Rhesus rotavirus type-A or 0.9% NaCl (normal saline) intraperitoneally within 24 hours of birth to induce experimental model of biliary atresia. The extrahepatic bile ducts including gallbladder were microdissected en bloc at 3, 7 and 14 days after rhesus rotavirus or saline injection. TaqManM-BM-. Array Rodent MicroRNA Card v2.0 (A and B) were used to screen microRNAs whose expression was differently regulated after rhusus rotavirus injection compare to the normal saline controls. microRNA expression profiling. Each experimental conditon has 3 sets samples . Two to six extrahepatic bileducts were pooled prior to total RNA isolation depending on the size to ensure adequate RNA quantities to perform experiments quantifying microRNA expression.
Project description:We addressed the potential for global regulation of miRNA biogenesis by BDNF using miRNA arrays that selectively measure mature miRNA, as opposed to pre-miRNA. Hippocampal neurons were treated with BDNF for 30 min in the presence of Actinomycin-D to assess changes due to processing of existing pre-miRNAs rather than new pre-miRNA production. We used Applied Biosystems 7900HT Fast Real-Time PCR system using Taqman Rodent MicroRNA Array A. Data is from three paired BDNF and Mock experiments (1,2,3). Each array (TaqMan) contained 375 rodent miRNA targets of which 195 were detectable in hippocampus in three independent paired experiments.
Project description:We investigated whether biomarker analysis in endobronchial epithelial lining fluid (ELF) collected by bronchoscopic microsampling may be useful for a definitive preoperative diagnosis. Therefore we compared ELF samples close to nodule and from the contralateral site from patients with malignant or benign diagnosis. ELF samples have been derived from early stage NSCLC patients and controls. Wilcox Test was performed to identify differentially expressed genes associated to a malignant diagnosis. key words: disease subtype analysis