Affymetrix Microarray Service
The Genomics Core Facility processes RNA and DNA for hybridization to Affymetrix arrays such as 3' IVT arrays, Gene ST arrays and tiling arrays to investigate global gene expression as well as the transcriptional profiling in a wide range of organisms. Depending on the array type the amount of required input nucleic supplied by the interested experimentator varies from less than 50 ng to several ug. Each nucleic acid sample will be analyzed for its quality and quantity, amplified, fragmented, and terminally labeled before being hybridized to an array, following a standardized protocol. Bound nucleic acids will be visualized by fluorescent dye conjugated antibody detection of biotinylated nucleic acid using a powerful high resolution scanner. The end user will be provided with "Cel" files containing all experimental data required for end user bioinformatics analysis.
If desired, the Core Facility can also provide data analysis for expression arrays using Partek's Genomics Suite software. Please contact the facility to discuss any planned microarray projects.
Nucleic Acids analysis with Agilent Bioanalyzer:
The Core Facility staff offers analysis of nucleic acid samples (both RNA and DNA) using the Agilent 2100 Bioanalyzer. This instrument provides an objective measure of nucleic acid quality that is more informative than traditional agarose gel results, is faster, and eliminates the use of ethidium bromide. The bioanalyzer chip uses microfluidics technology and voltage induced size separation in gel-filled chambers detecting nucleic acids with laser induced fluorescence. The resulting electropherogram trace is converted into a gel like image. For RNA, the Agilent software computes a RNA Integrity Number (RIN) using a number of features from the electropherogram, such as the ratio of 28S to 18S ribosomal RNA. This value provides a qualitative assessment of the RNA. DNA assays on the bioanalyzer can be used to assess the size and purity of DNA for downstream applications such as cloning or NextGen sequencing.
The user provides samples at the required concentration and Core Facility staff will run the samples on the bioanalyzer chip and email the results to the user in a easily viewable PDF file format. Analysis can usually be arranged within 2 business days. Please contact the facility staff for specifics on sample preparation.
Illumina Next Generation Sequencing:
As of May 2010, the Core Facility offers Next Generation sequencing services on a GAIIx instrument. We are expanding services in March 2011 to offer sequencing using the HiSeq 2000 instrument. Currently the Core Facility accepts user prepared libraries for Next Generation sequencing. The submitted samples will be analyzed for quantity and quality using KAPA qPCR and a Bioanalyzer. Samples which pass the QC measures will then be amplified on a flowcell using a cluster robot (cBot), followed by sequencing on the GAIIx or the HiSeq 2000. The Core Facility offers currently both single and paired end runs with read length options from 35 to 100 bp.