454 / Illumina Sequencing


CUGI works with several external partners to deliver 454 and Illumina sequencing.

Affymetrix Services

CUGI now offers a complement of Affymetrix services using the GeneChip® Scanner 3000 7G platform and two GeneChip® Fluidics Station 450s.

BAC Library Construction

CUGI has extensive experience in creating custom large insert BAC libraries with average insert sizes generally ranging between 120 and 160kb. CUGI has produced numerous plant, animal and microbial BAC libraries encompassing many different taxa in the tree of life, many of which are available through our online ordering system.

Capillary Fragment Sizing

CUGI offers capillary fragment sizing of fluorescent labeled fragments on our ABI 3130xl or ABI3730xl DNA Analyzers. Please contact CUGI for an exact quote for available spectrals and custom projects.

cDNA Library Construction

CUGI produces high quality full-length cDNA libraries. The libraries are well-suited for EST sequencing and other gene discovery applications.

Colony Picking


CUGI employs two state-of-the-art Genetix Q-bots for colony picking, library replication, and filter gridding.

Copy Number Analysis


The Affymetrix Genome-Wide Human SNP Array 6.0 features 1.8 million genetic markers, including more than 906,600 single nucleotide polymorphisms (SNPs) and more than 946,000 probes for the detection of copy number variation. This chip is a valuable tool for exploring the role of copy number in human disease.

Custom Array Analysis

Affymetrix's MyGeneChip™ Custom Array Program provide highest-resolution data on a single array, tailored to your specific research needs. Custom Arrays offer an expanded selection of custom solutions, including whole-transcript expression, exon analysis, ChIP-on-chip, transcript mapping, SNP discovery, 3' expression, resequencing, and whole-genome genotyping.

DNA Hybridization


CUGI employs DNA hybridization using radioisotopes and BAC macroarrays to identify corresponding genomic regions in BAC libraries. We offer single probes and custom pools up to 125 markers at a time. This is an invaluable tool to identify genes or regions of interest and integrate genetic information into a physical context. Please contact CUGI for an exact quote for a project.

EST Analysis

CUGI's bioinformatics staff is available to perform basic and customized analysis of ESTs ranging from pre-processing and assembly to functional annotation.

Fosmid Library Construction

CUGI now offers high quality fosmid library construction. Fosmids are commonly used for preparing genomic libraries when a smaller insert size is desired. The inserts have an average size of 40 kb and are produced by random shearing, yielding a more uniform coverage of the genome than other library types. Fosmids are excellent candidates for closing gaps in a whole genome sequence and physical maps due to their uniform coverage. Additionally, they are popular for metagenomic and expression studies.

Gene Expression Analysis


With the Affymetrix GeneScan® Scanner 3000 7G platform CUGI provides whole-transcript or 3' IVT gene expression profiling of whole or partial genomes using existing Affymetrix microarrays.

Gene Regulation Analysis

Affymetrix GeneChip® Tiling Arrays are comprehensive arrays available for discovering novel RNA transcripts (transcript mapping) or mapping sites of protein/DNA interaction in chromatin immunoprecipitation experiments (ChIP-on-Chip).

Genomic Database Construction

A strength of CUGI bioinfomatics is in the area of construction and management of online genomic databases.

GWAS and Genotyping

The Affymetrix GeneChip® SNP array can be used for genotyping and/or for identifying genetic associations with traits across a given genome, also known as genome-wide association study (GWAS).

High Information Content Fingerprinting


CUGI is one of a few labs that specializes in physical mapping by High-Information Content Fingerprinting (HICF). The technique uses 5 restriction enzymes, fluorescent labeling of fragments and fragment sizing via capillary electrophoresis. We also specialize in contig assembly/analysis, and employ a unique marker pooling strategy to anchor genetic information to a physical framework. Collectively, an integrated physical/genetic framework provides a superhighway for structural, functional, and evolutionary genomics research.

Library Plate Replication

CUGI offers library plate replication which includes: the plate, media, bar-coded label and freezer storage boxes for the plates. The center can replicate over 250 master plates into 2 individual replicas per day. Please contact CUGI for an exact quote for a project.

Macro-Arraying (Gridding)


CUGI grids libraries from microtitre plates onto Hybond N+ membrane (filters) in high-density colony filter arrays using Genetix Q-Bots. The current production rate is a maximum of 90 filters per day.

Marker Mining

A combination of in-house scripts and publicly available software applications have been developed to mine SSRs and SNPs from Sanger-style or next generation sequence sets.

miRNA Profiling


The Affymetrix GeneChip® miRNA array supports miRNA coverage for more than 70 organisms. CUGI provides analysis of Affymetrix miRNA chips using an Affymetrix GeneChip® Scanner 3000 7G.

Next-Gen Sequence Assembly

CUGI bioinformaticists have experience assembling short reads from genomic DNA and ESTs.

Physical Mapping

CUGI specializes in physical mapping via High-information Content Fingerprinting (HICF). Our bioinformatics staff has experience in assembling and analyzing HICF fragment data to construct high quality physical maps.

Re-arraying Libraries


CUGI re-arrays libraries robotically using a selected list of clones which are entered into the Q-Bot's computer. Then clones selectively picked from the original library plates and placed in new microtitre plates to create a replicated re-arrayed version of the library. This can be done in both 96 and 384-well formats. Charges are project specific and quotes can be obtained by contacting CUGI for an exact quote for a project.

Sanger Sequencing

CUGI offers high quality Sanger-style sequencing with fast turnaround times. Our services range from DNA isolation from host cells to sequencing of purified plasmids and PCR products. We operate on both high and low throughput platforms and can accommodate single samples to large scale sequencing projects. Our ABI sequencers offer superior quality and long reads. We also offer a suite of sequence assembly and analysis options, please see our options in our Bioinformatics section for a list of services. Sequencing orders may be placed through our online ordering system.

Sequencing QA/Trimming

An in-house pipeline has been constructed at CUGI for the Quality Analysis (QA) and Trimming of Sanger-style genomic and transcriptomic data.

Shotgun Library Construction

CUGI also offers small-insert or shotgun library production. High quality random-sheared shotgun libraries of BAC clones and whole genomes are regularly produced at CUGI. These libraries typically consist of inserts ranging from 1-10kb and are used extensively in DNA sequencing and mapping projects throughout the world.

Storage & Distribution of Clones

Libraries may be deposited at CUGI for public distribution to commercial entities and public institutions. Clones are sold at standard CUGI prices. Researchers may place orders for copies of the library, individual clones, or filter sets through our online ordering system. CUGI also offers BAC sequencing, filter hybridization, and sequencing services.

Tripal Customizations


Tripal is a collection of open-source freely available Drupal modules under development at CUGI. These modules serve as a web interface for the GMOD Chado database. Tripal is a part of the GMOD family of tools.

Whole BAC Assembly/Gap Closure/Finishing

As an extension to our shotgun library construction and sequencing services, CUGI offers assembly, gap closure and finishing of whole BACs. Sequence data may be generated at CUGI from an external sequencing facility.