Project description:Plant small RNAs are a diverse and complex set of molecules, ranging in length from 21 to 24 nt, involved in a wide range of essential biological processes. Nowadays, high-throughput sequencing is the most commonly used method for the discovery and quantification of small RNAs. However, it is known that several biases can occur during the preparation of small RNA libraries, especially using low input RNA. We used two types of plant biological samples to evaluate the performance of seven commercially available methods for small RNA library construction, using different RNA input amounts. We show that when working with plant material, library construction methods have differing capabilities to capture small RNAs, and that different library construction methods provide better results when applied to the detection of microRNAs, phased small RNAs, or tRNA-derived fragments.
Project description:Purpose: To know the expression of all cytochrome P450 (CYP) enzymes and related drug metabolizing enzymes in pancreatic cancer models Methods: We obtained expression profiles of 8 commercially-available pancreatic cancer cell lines and one non-cancerous immortalized cell line by RNA-sequencing. The pancreatic cancer cells were compared among themselves and to the non-cancerous control cells. Results: We confirmed reports that CYP3A5 is highly overexpressed in pancreatic cancer models, and additionally report that known xenobiotic-metabolizing CYPs are lowly expressed in comparison.
Project description:Commercially available human genomic microarrays from four different manufacturers were used to compare Human Brain Total RNA against Universal Human Reference RNA (both commercially available) prepared at two different starting amounts (20 µg or 1µg). For each level of RNA, 6 replicates were performed with Human Brain Total RNA labelled with Cy3, and Universal Human Reference RNA labelled with Cy5. The labelling was then reversed (dye flip) creating another 6 replicates. This meant that for each of the four manufacturers there were a total of 24 arrays. Image processing was performed with two different software packages, and data was normalized with three different strategies.
Project description:Commercially available human genomic microarrays from four different manufacturers were used to compare Human Brain Total RNA against Universal Human Reference RNA (both commercially available) prepared at two different starting amounts (20 µg or 1µg). For each level of RNA, 6 replicates were performed with Human Brain Total RNA labelled with Cy3, and Universal Human Reference RNA labelled with Cy5. The labelling was then reversed (dye flip) creating another 6 replicates. This meant that for each of the four manufacturers there were a total of 24 arrays. Image processing was performed with two different software packages, and data was normalized with three different strategies.
Project description:Malignant mesothelioma (MM) is an aggressive, fatal tumour strongly associated with asbestos exposure. There is an urgent need to improve MM patient outcomes and this requires functionally validated pre-clinical models. Mesothelioma-derived cell lines provide an essential and robust tool widely used for candidate drug evaluation. Although a number of cell lines are commercially available, a detailed comparison of these lines with freshly-derived primary tumour cells to validate their suitability as pre-clinical models is lacking. Patient-derived primary mesothelioma cell lines were established and characterised by gene expression profiling. Molecular profiling revealed a significantly different transcriptome in commercially available compared with primary cell lines. Primary mesothelioma cell lines are more representative of the tumour close to its native state and show a degree of molecular diversity, thus capturing the disease heterogeneity in a patient cohort.