Explore Available Analyses
- Affymetrix gene array data (anchored and explorative)
- PCR-based (SABioscience PCR) array data
- Selected custom expression data evaluation
- Protein expression data
- Single-cell RNAseq data analysis
- microRNA expression data
- Long non-coding RNA data
- Explorative evaluation of IPA curated information within any experimental system
Gene arrays are used to simultaneously evaluate mRNA levels of a large number of genes in a tissue sample, ranging from as few as ~50 to the transcriptional activity of the entire genome. The data are sample transcript levels and typically compared between test and control groups. In the case of Affymetrix data, we use the Affymetrix Expression Console software evaluation in addition to our own to determine data quality. We evaluate data quality and perform a core analysis using the Ingenuity Pathway Analysis (IPA) software that includes a standardized report for most significantly altered transcripts and the underlying upstream regulation present in a system customized fashion.
Advanced IPA functions are available by request.
siRNA design and data evaluation
Effective siRNA design is a crucial tool in molecular biology that allows for the evaluation of loss-of-function in an experimental context. Information on desired target is needed to custom design siRNA(s) with the greatest chance of effective gene silencing. We will design up to three (within the confines of possible targetability) siRNAs according to our published methods, and we will provide the actual sequences in return.
In vivo siRNA experimental design and implementation
In vivo delivery of siRNA in animal models is costly, both due to amount of reagent needed and the inherent limitations of delivery. We need information of experimental design and intended target population to evaluate the best approach for the model system (animals or tissue culture). Information on delivery method, assistance with design and interpretation of data are provided on a customized basis. Model systems that cannot currently be used will not be evaluated and no charge incurred.
microRNA PCR design and verification
Determination of microRNA (miR) levels in samples is one initial step to clarify gene expression regulation in some experimental models. With the knowledge of the miR target, we custom design a PCR-based assay typically sensitive from 10 to 106 miR copies per reaction. Data analysis includes a standard curve for the entire linear range of the design, a graphical representation of normalized miR copy number for each sample and a list of probable miR targets in a basic network drawn from IPA. In-depth analysis of complex interactions is available upon request.
PCR robustness development and optimization using orthogonal array statistics
While PCR assays are a relatively quick and inexpensive means to quantify levels of nucleic acids in a biological sample, poor primer, target and assay design risks leaving the end user with an inaccurate tool. With a known RNA/DNA target in hand, our design expertise accounts for very robust designs, minimizing the risk for end-user- or equipment-dependent variability. Known or estimated samples are needed to provide statistical evaluation of the most robust conditions, and we provide the final optimized conditions for each parameter tested (typically concentrations of primers, Mg2+, template, dNTPs and amount of enzyme).
Quantitative probe (TaqMan) PCR design
Quantitative probe (also known as TaqMan) PCR involves primers designed for rapid amplification and adds a fluorescent probe within the target site used for quantification of target concentration in the sample. We need information on the target and the experimental design to most effectively provide up to three (within the confines of possible targetability) quantitative probe PCRs. Specific sequences for primers and probe are returned and one complimentary troubleshooting consultation is offered.
Primary and secondary DNA and RNA sequence analysis
Primary DNA and RNA sequence assembly and determination of known canonical sequences and secondary folding is an essential tool in determining gene expression regulation. We require sequence data only along with sample source and experimental design (if appropriate). Results include primary sequence information such as transcriptional binding sites and examples of transcripts with similar regulatory elements and secondary structure/folding information relevant to the transcriptional regulation and/or experimental design.
Information on available drugs and targets in the context of model building
This is an adjunct service to network and model building where we determine the availability of drugs (some in clinical trials, other commercially available) and other reagents (including naturally occurring compounds) where available.
Flowcytometric analysis of tagged pathogen gene expression in vivo
This requires investigator-supplied reagents from which a flowcytometric assay is designed according to our published methods. This is suitable to determine drug/compound effects of a given pathogen and is currently limited to BSL-2 and below.
Generation of custom-designed, publication quality figures
This is an adjunct to all our services, where we produce publication quality graphical output according to specifications (any journal, poster formats or presentation software specific). As is evident from our numerous publications, we are familiar with this process and use the latest available software for these purposes.