Genomic Profiling Shared Resource
(Lisa White, Ph.D., Director)
- Our goal is to provide investigators access to state-of-the-art quality molecular profiling technology services for both transcriptional and genomic profiling, including microarray and next generation sequencing.
- Our purpose is to assist researchers in utilizing genomic profiling technology employing good experimental design, and providing data management and data analysis resources.
Experimental Design Consultation
All users of the DLDCC GPSR are required to meet with either the director to discuss their proposed research. These meeting 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 GPSR 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 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 GPSR 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 GPSR 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) as well as the Qubit. Genomic DNA samples are tested using the NanoDrop ND-1000 spectrophotometer and integrity is assessed using agarose gel electrophoresis.
Illumina Genome Analyzer II Next Generation Sequencing
This Illumina technology detects single transcripts per cell in 1 g of total RNA or less. The simple workflow allows users to quickly generate full sequence from any poly-A tailed RNA to analyze novel transcripts, novel isoforms, alternative splice sites, rare transcripts and coding SNPs.
Researchers can easily expand the scale of their study to identify binding sites across the entire genome simultaneously using Illumina’s ChIP-Seq. Oligonucleotide adapters are added to the small fragments of DNA that were bound to the protein of interest to enable sequencing. The Genome Analyzer sequences ChIP-isolated DNA fragments to allow researchers to identify and quantify the sites bound by a protein of interest. Users can study modifications such as transcription factors, polymerases and transcriptional machinery.
Randomly fragmented genomic DNA is attached to planar, optically transparent flowcell. Attached DNA fragments are extended and bridge amplified to create hundreds of millions of clusters. DNA-Seq enables whole-genome sequencing and resequencing, SNP discovery, identification of copy number variations and chromosomal rearrangements.
- Small RNA-Seq
Illumina’s platform offers small RNA discovery and analysis using Genome Analyzer II. This application enables small RNA profiling in any organism, allowing researchers to find novel small RNAs, characterize mutations and analyze expression of all small RNAs in each sample. The platform can profile approximately 20 million small RNA sequences in each flow cell.
- HiSeq 2000
- Genome Analyzer IIx
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 GPSR. 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.
- Quantitative Real-Time PCR Gene Expression platform
Users can access Real Time Quantitative PCR (QCPR) services at the GPSR. QPCR allows users to validate gene expression data obtained with arrays as well as to confirm copy number changes identified in their samples. Specific primers and Taqman probes will be designed using PrimerExpress software from Applied Biosystems Inc (ABI). The specificity and uniqueness of the primers will be further checked using in-silico PCR software. The oligos will be synthesized either by ABI or the molecular biology core laboratory in BCM. RNA samples will be reversed transcribed to cDNA using reverse transcription kit from ABI. The primers, probes, DNA or cDNA samples will be put into either the ABI 7000 Prism real time PCR machine or BioRad Icycler real time PCR machine for generation of Ct values. Samples are duplicated in adjacent wells and average Ct will be scored upon completion of the reactions.
Genomic DNA-Based Profiling
- SNP Genotyping Platform
DLDCC members can utilize the Affymetrix SNP 6.0 Genechip (1.8 million probe array) through the GPSR. SNP Genotyping can be used for gene association studies as well as studies assaying copy number changes in samples (or array CGH). Illumina assays for SNP genotyping include the Infinium assay and GoldenGate assay. The platform allows for whole genome SNP analysis, focused and custom SNP genotyping, linkage analysis, and methylation profiling.
- Array Comparative Genomic Hybridization (aCGH)
Genomic copy number changes can be assayed using several platforms in the GPSR including Agilent, Nimblegen, and Affymetrix SNP 6.0, or Illumina SNP arrays. Chromosomes are known to have numerous different copy number aberrations in cancerous cells and many researchers are now utilizing this service.
- Protein-Nucleic Acid and Epigenomic arrays
The GPSR 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), Nimblegen (whole genome tiling, custom tiling), and Illumina arrays.
The GPSR works in conjunction with the DLDCC 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 GPSR and they include aCGH analysis, miRNA expression analysis, and Illumina bead-array analysis.
Charge Back Fees and Forms
- GPSR service pricing can be accessed in this fee table. Or investigators can send an e-mail to firstname.lastname@example.org to receive pricing information.
- New investigators (first time users of the GPSR) should fill out the MAID PI Registration form and fax it to the GPSR. Once a user is registered in MAID they will be able to submit services requests online.
- MAID can be accessed at MAID Login. A MAID user guide is also available.
Lisa D. White, Ph.D.
Director, Genomic Profiling Shared Resource, Dan L. Duncan Cancer Center
Asst. Professor, Dept. Molecular & Human Genetics
Director, Microarray Core Facility
Technical Director, Chromosomal Microarray Analysis, Molecular Genetics Laboratory
Baylor College of Medicine
One Baylor Plaza, Rm. 333E, Mailstop: BCM225
Houston, TX 77030
Tel: 713-798-7607 Fax: 713-798-7610
Director: Lisa D. White, Ph.D.
Bioinformatician: Horatiu Voicu, Ph.D. Administrative Contact: Maria Rodriguez
Laboratory Manager: Laura Liles Laboratory Supervisor: Mylinh Bernardi
Research Assistant I: Kelsea Boran Research Technician III: Rene Sheffer Research Assistant I: Rebecca Thornton IT Infrastructure: Richard Sucgang, Ph.D.
Computer System Administrator: Carl Broadbent
Baylor College of Medicine
One Baylor Plaza, Room 325E
Mail Stop: BCM225
Houston TX, 77030
• Main BCM Lab: 713-798-7699
• Main BCM Fax: 713-798-7610
Web site links
For more information on services in the BCM-GPSR, visit: the microarray Web site.