Gene Expression Analysis Comparing Two RNA Isolation Methods from Recent and Older Archived Formalin-Fixed, Paraffin-Embedded Tissue (FFPET) Samples

31 Oct 2012

Formalin-fixed, paraffin-embedded (FFPE) tissue samples are widely available for retrospective studies. However the quantity and the quality of the isolated RNA can limit downstream applications. In addition to tissue fixation, subsequent storage time of the tissue blocks is one of the main factors that can influence the quality and quantity of the isolated nucleic acids, as long-term storage can result in lower yield. In this application note from Roche a comparative study using two commercially available kits for RNA isolation from FFPE tissue using older archived and recent tissue samples is presented. For testing the downstream applicability of the isolated samples, gene expression of three recently identified colorectal cancer-specific discriminatory transcripts was determined using real-time PCR.

Tags

BiosensorsBiosensors are devices used to detect an analyte using biological molecules specific to the analyte coupled to a detector. Biosensor instruments may be photometric, typically using surface plasma resonance (SPR), electrochemical or QCM (quartz crystal microbalance) biosensors. Biosensors should be selective, portable, robust and sensitive and have a fast response time. Systems may be manual or automated and usually have associated software.Cell / Tissue CultureCell culture or tissue culture is used to study the biology of cells or tissues and to isolate cellular products in an environment which can be manipulated and well defined. Accurately control your culture environment with bioreactors or culture incubators, bind your cells to a surface or together with an extracellular matrix. Distinguish cell types with differential media or proliferate cells with certain characteristics using selective media. Enrich your media with supplements such as growth factors, sera and vitamins. Find the best cell and tissue culture products, kits and equipment in our peer-reviewed product directory: compare products, check customer reviews and receive pricing direct from manufacturers.PCR and Thermal CyclingPolymerase chain reaction (PCR) kits and thermal cyclers are used for the in vitro amplification of DNA permitting subsequent analysis and experimental procedures. Explore a range of high-quality polymerase, primers and nucleotides or simplify your workflow with a PCR mastermix. Find reverse transcription PCR (RT-PCR) and cDNA synthesis kits for RNA products and libraries. Quantitatively measure the amplification of DNA with real-time PCR (qPCR) and droplet digital PCR (ddPCR) kits and systems, and discover automated PCR setup solutions to increase throughput. Alternative DNA amplification methods also include recombinase polymerase amplification (RPA) kits. Find the best PCR kits and thermal cyclers and purification equipment in our peer-reviewed product directory: compare products, check customer reviews and receive pricing direct from manufacturers.Medicinal ChemistryMedicinal chemistry is a broad discipline encompassing the design, identification, synthesis and development of chemicals in drug discovery. It includes a number of techniques covering structural biology, synthetic chemistry and molecular biology. Technologies used in medicinal chemistry include ADME, lab-on-a-chip, high content screening and assay assembly.Cell-Based AssaysCell-based assays are used to monitor the presence, quantity and activities of a desired cellular analyte including drug molecules or biomarkers. This can reveal information on cell health (apoptosis, cytotoxicity, viability and proliferation assays), cell metabolism, cell migration and cell signaling mechanisms. Find the best cell-based assay products, kits and equipment with our peer reviewed product directory: compare products, check customer reviews and receiving pricing direct from manufacturers.DNA / RNA Extraction and PurificationPurified DNA and RNA are required for numerous downstream molecular biology applications. Consequently, the importance of high-quality DNA/RNA extraction and purification equipment cannot be underestimated. Many purification kits are available and are typically optimized for nucleic acid type and source, including plasmid DNA, genomic DNA, mRNA, RNA and viral nucleic acid purification kits. Automated extraction and purification of nucleic acids can be implemented with magnetic bead separator instruments or high-throughput purification workstations. Find the best DNA/RNA extraction and purification equipment in our peer-reviewed product directory: compare products, check customer reviews and receive pricing direct from manufacturers.DNA SequencingDNA sequencing, such as sanger sequencing, is a biological technique that determines the precise order of nucleotide bases in a fragment or template of DNA. DNA sequencers and genetic analyzers are based on capillary electrophoresis, where labeled DNA fragments are electrophoretically separated by size as they migrate through a polymer. Find the best DNA sequencing products, including DNA sequencing kits, genomic libraries and genetic identity kits in our peer-reviewed product directory: compare products, check customer reviews and receive pricing direct from manufacturers.Protein CrystallographyProtein crystallization is the process of crystallizing purified proteins for 3D structure analysis by x-ray crystallography. The main methods of protein crystallization include sitting drop, hanging drop and microbatch. It is important to control parameters such as pH, temperature and concentration. Following crystallization, detectors and software are used for data collection and analysis.Gene Expression and Molecular CloningMolecular cloning is a set of techniques that utilizes vectors to transfer recombinant DNA into host cells and is an essential tool for investigating the expression of genes and proteins in bacterial or mammalian cells. A variety of vectors optimized for gene cloning and expression in a range of host organisms are available, alongside competent cells for genetic replication. Here, you can explore a range of molecular tools, high-quality genomic and cDNA libraries, premade clones, transformation and transfection reagents and mutagenesis or gene expression detection assays and expression arrays. Find the best gene expression and molecular cloning products in our peer-reviewed product directory: compare products, check customer reviews and receive pricing direct from manufacturers.Next Generation SequencingNext-generation sequencing (NGS), also known as whole-genome sequencing, high-throughput sequencing and massive parallel sequencing, produces and analyses thousands to millions of nucleotide sequences at once. Sequencing systems operate via varying technologies depending on the manufacturer, including sequencing by synthesis, ligation, pyrosequencing, ion semiconductor and single-molecule real-time sequencing. For NGS, library preparation is paramount to successful sequencing. In this section, explore a range of library preparation kits, from targeted, amplicon-based or hybridization-based kits including epigenomic, transcriptomic and genomic workflows to fragmentation kits. Find the best next-generation sequencing products in our peer-reviewed product directory: compare products, check customer reviews and receive pricing direct from manufacturers.Tissue ProcessingTissue processing involves preparing biological tissue samples for microscopic analysis, including fixation, embedding, and sectioning. This process is essential for histopathology and diagnostic applications. Explore tissue processing products in our peer-reviewed product directory; compare products, check reviews, and get pricing directly from manufacturers.Cancer ResearchAlthough cancer is often referred to as a single condition, it actually consists of more than 100 different diseases. Microscopy, mass spectrometry, high throughput sequencing and flow cytometry are some of the most common techniques employed in cancer research labs.Gene ExpressionReal-Time PCRReal-time PCR (RT-PCR) is a technique used to amplify and simultaneously quantify nucleic acids in real time. It is a key tool in gene expression analysis, pathogen detection, and diagnostics. RT-PCR allows for the detection of specific RNA or DNA sequences with high sensitivity and specificity. Browse our peer-reviewed product directory to find the best Real-Time PCR systems; compare products, check reviews, and get pricing directly from manufacturers.FFPEFormalin-fixed paraffin-embedded (FFPE) tissues are commonly used in medical research, particularly in histology and cancer studies. The preservation process allows long-term storage of tissue samples for later analysis. Explore FFPE research products in our peer-reviewed product directory; compare products, check reviews, and get pricing directly from manufacturers.