Services offered by the Functional Genomics Core
Microarrays available to DDRCC members
DNA Microarrays
Agilent human whole genome array (1x44K, 4x44K)Human microRNA array (link)
The Human miRNA Microarray contains probes for 470 human and 64 human viral microRNAs from the Sanger database v9.1. Integrating Agilent's probe design and unique labeling methods, this microarray delivers robust data with a simple, streamlined protocol. The generation of complete miRNA expression profiles using robust and highly sensitive microarrays allows broad insight into human miRNA expression and regulation.The CHIP-on-chip microarrays (link)
The CHIP-on-chip arrays (chromatin immunoprecipitation-on-chip) allow the monitoring of binding events of DNA-binding proteins to areas around the human and mouse promoters, yeast genome and defined regions such as the human ENCODE region.Protein Arrays (link)
ExcelArray antibody sandwich microarrays are multiplexed fluorescent immunoassays for the simultaneous quantitation of up to 12 protein targets. Each ExcelArray slide contains 16 wells (subarrays) printed with specific antibodies, a negative control and a positive control all spotted in triplicate. Each slide can be used to analyze 10 samples when the 6 point standard curve is used. The protocol is a simple sandwich ELISA format that uses a Pierce DyLight 649 conjugate for detection and is compatible with conventional fluorescent slide readers. The ExcelArray microarray platform offers excellent sensitivity, low background, increased dynamic range, excellent signal to noise ratios and excellent reproducibility in complete and easy to use kits.
Target Labeling, Hybridization and Scanning for DNA Microarray Experiments
If the amount of starting RNA is in ng (minimum 50 ng) range, linear amplification of RNA will be performed with Agilent low RNA input fluorescent linear amplification kit.
Experimental Design for Protein Array Experiments
Sample Types The protein array kit has been optimized for serum, plasma and cell culture supernatants. We recommend diluting serum and plasma samples 1:3 and cell culture supernatants 1:1 with Assay Diluent.Quantitative assays
The protein array kit includes purified cytokines for building a five-point standard curve covering the range of 15 pg/ml to 800 pg/ml. By comparing signals of unknown samples to the curve, the concentration of each cytokine can be estimated. The standard curve requires six wells, leaving 10 wells for experimental samples.Qualitative assays
For qualitative comparisons among samples, 15 wells of the 16-well array can be devoted to an experimental sample (one well reserved for a blank well). Comparisons should be made among the average signals from each cytokine in each well.Data Retrieval
Your data including tiff images will be transferred to you on a CD-ROM. Normally, you should expect to receive you data back in about one week after you submit your sample. We provide array service to DDRCC member on a first-come, first-served basis.Data Analysis
The Genomics Core provides support for both introductory and advanced data analysis. For introductory data analysis, we assist investigators to be familiar with their array data output format, generate differentially expressed gene list. GenePix Pro 4.1 is available in the Core if you wish to use the software to explore your data. Please sign up in the Core to use the software. If you have more than one array data and would like to do advanced data analysis such as statistical test differentially expressed genes, clustering genes/experimets, we provide assistant for these softwares: BRB-Array Tools, SAM and Acuity 3.0 from Axon Instrument. If you would like to visualize gene expression and other genomic data on maps representing biological pathways, we provide support for GenMAPP software.