The Diabetes and Endocrinology Microarray Resource, Biostatistics, and Bioinformatics
The DRC Microarray Shared Resource provides researchers access to state-of-the-art molecular profiling technology and services. This facility:
- Serves as the source for experimental design consultation, probe preparation protocols, and image scanning for spotted glass arrays (Agilent and NimbleGen) as well as Affymetrix GeneChips®
- Provides a secure web-based online environment for service requests, sample tracking, data management and billing in the form of Micro Array Information Database, or MAID, our award-winning microarray information database.
Experimental Design Consultation
All users of the DRC MARBB are required to meet with the director to discuss their proposed research. These meetings are generally for one hour and include explanations of the different array technology options available to the user and strategies on how the different array applications will benefit the user's research. At this time, pricing is also discussed with the user and experiments are designed that maximizes the numbers of samples to achieve the most power while keeping the experiment affordable to each user.
Clone Repository Services
The MARBB owns thousands of cDNA clones and these are provided by request to investigators. Users can search our Mouse and Human clone sets for genes they are interested in for use in verifying results from gene expression or other experiments. Clone sets are listed below and can be searched through the core website. Mouse NIA 15K, Mouse BMAP 32K, Mouse BMAP Retina, Mouse NIA 7.4K, Mouse 3.5K Pancreas, Mouse RIKEN FANTOM1 21K, Human HTVV 40K (sequence verified). The MARBB has implemented a web-based clone search since the P30 submission that makes identifying the cDNA clone of interest easy and efficient.
Sample Quality Assurance/Quality Control
Sample quality is one of the most important factors for producing good data. All users intending to utilize one of the genomic profiling services offered in the MARBB must submit the samples to the facility prior to requesting other services. This service is also open to users who just want to gauge the quality of their sample without using our other services. Samples are submitted to the facility through our web-based LIMS and tested for integrity, concentration, and purity. RNA and cDNA samples are analyzed on the Agilent 2100 Bioanalyzer (Agilent Technologies) that utilizes Lab-on-a-Chip technology (Caliper Life Sciences) and the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies). Genomic DNA samples are tested using the NanoDrop ND-1000 spectrophotometer and integrity is assessed using agarose gel electrophoresis.
Gene Expression Profiling
Affymetrix gene expression profiling
This GeneChip platform is a commercially available DNA-based silicon wafer populated with oligonucleotides that represent the genes and expressed sequence tags (EST) currently known for a particular genome. Arrays are available in a variety of species, although the most frequently used in our facility are mouse, human, and rat. Gene expression applications are: whole genome transcriptome analysis, alternative splicing analysis, and whole genome tiling. There are two labeling technologies for these applications, the Eberwine 3' IVT and a whole transcriptome labeling coupled with ribosome reduction.
Spotted glass array-based expression profiling
We offer several spotted glass array platforms for gene expression profiling including Agilent, and NimbleGen. Samples can be analyzed with one or two color labeling. Again, multiple species-specific arrays are available for use to our users with the majority use being human and mouse. Nimblegen arrays are used almost exclusively for prokaryotic profiling. In addition to classical profiling, we also offer microRNA profiling using Agilent or Exiqon arrays.
Luminex bead-based expression profiling
Multiplex expression analysis utilizing Luminex beads is available through the MARBB. This technology allows us to offer customized bead panels to measure expression of mRNA (Panomics) and microRNAs (FlexmiR). This is a robust platform that will enable researchers to measure expression of a select number of genes at a reasonable price.
SuperArray QPCR Gene Expression platform
The GSPR is now offering SuperArray Bioscience services. These 96-well QPCR arrays provide researchers access to new tools for profiling gene expression focused on a biological pathway or disease state. The RT2 Profiler PCR Array System allows researchers to easily determine changes in gene expression for up to 96 genes of interest. Over 100 PCR Arrays are available covering Cytokines, Apoptosis, Cancer, Signal Transduction, and many other topics. They are also easily customized to fit any list of genes.
Genomic DNA-Based Profiling
SNP Genotyping Platform
DRC members can utilize the Affymetrix SNP 6.0 Genechip (1.8 million probe array) through the MARBB. SNP Genotyping can be used for gene association studies as well as studies assaying copy number changes in samples (or array CGH).
Array Comparative Genomic Hybridization (aCGH)
Genomic copy number changes can be assayed using several platforms in the MARBB including Agilent, Nimblegen, and Affymetrix SNP 6.0. Chromosomes are known to have numerous different copy number aberrations in cancerous cells and many researchers are now utilizing this service.
DNA-based arrays (not aCGH)
The MARBB also offers ChIP-chip analysis for protein-DNA interactions as well as assaying epigenetic changes such as methylation and chromatin modeling. Platforms available to assay ChIP-chip and methylation, etc. are Affymetrix (whole genome tiling, promoter), Agilent (promoter, custom tiling), and Nimblegen (whole genome tiling, custom tiling).
The MARBB works in conjunction with the Biostatistics Shared Resource. Users who intend to request data analysis (for SNP genotyping and mRNA expression) help are directed to the Biostatistics Resource for discussions that includes experimental design/consultation. Other analyses are available through the MARBB and they include aCGH analysis, miRNA expression analysis, and Illumina bead-array analysis. The MARBB also collaborates closely the with Bioinformatics Research Center here at BCM for aid in pathway analysis and other database-related issues.
Pricing for services in the MARBB can be found on the Genomic and RNA Profiling Core or GARP (formerly the Microarray Core Facility) website.
- Lisa D. White, Ph.D., Director
- Maria Rodriguez, Administrative Contact