UNC Genomics Core Facilities and Resources

 

These pages list our core facilities by areas of focus.  These are brief profiles of the cores; to find more detailed information on each core, including location, contact information, and equipment lists, please check out the facility overview in each core facility listing in our searchable database.


UNC provides a full spectrum of genomics based services. From multiple microarray platforms, multiple high throughput sequencing systems, real time PCR and in situ hybridization support, UNC has a highly skilled core facility that can meet most needs.

Genotyping


Functional Genomics Core performs expression profiling and SNP genotyping (Affymetrix) services.  We currently have Beckman Coulter's Biomek® FXP Target Prep Express robot and the GeneTitan Instrument from Affymetrix which allow the processing of hundreds of microarray samples in a week, and processing of high throughput expression peg arrays and Axiom genotyping high throughput peg arrays.  Also, we have the Affymetrix GeneChip® Scanner 3000 7G Plus Targeted Genotyping System in the Core.  It has the ability to scan all research arrays manufactured by Affymetrix including the high density expression arrays which place an entire genome on one GeneChip®.  This equipment includes 2 Fluidics Station 450s and the GeneChip® Hybidization Oven 640.


Mammalian Genotyping Core provides ABI TaqMan SNP Genotyping and Illumina BeadArray Genotyping services.


Lineberger Comprehensive Cancer Center Genomics Core provides microarray and DNA-library preparation services to assist researchers analyze gene expression and gene dosage changes by both microarray and mRNA-seq analysis.

Expression Analysis


Functional Genomics Core performs expression profiling and SNP genotyping (Affymetrix) services.  We currently have Beckman Coulter's Biomek® FXP Target Prep Express robot and the GeneTitan Instrument from Affymetrix which allow the processing of hundreds of microarray samples in a week, and processing of high throughput expression peg arrays and Axiom genotyping high throughput peg arrays.  Also, we have the Affymetrix GeneChip® Scanner 3000 7G Plus Targeted Genotyping System in the Core.  It has the ability to scan all research arrays manufactured by Affymetrix including the high density expression arrays which place an entire genome on one GeneChip®.  This equipment includes 2 Fluidics Station 450s and the GeneChip® Hybidization Oven 640.


Lineberger Comprehensive Cancer Center Genomics Core performs expression profiling and miRNA profiling using Agilent long oligonucleotide microarrays.


The Vironomics Core facilitates research at UNC by performing large-scale real time quantitative PCR reactions, amplicon generation and next generation sequencing using Roche 454 GS Junior (450 bp read length) and robot-assisted PCR in 96 and 384 well format. The Vironomics Core currently provides several real-time qPCR arrays for viruses and miRNAs profiling including: KSHV, EBV, HSV1 and HSV2, RRV, HCMV, NFkappaB, Pre-miRNA, and P53response12. The Roche 454 GS Junior sequencing is not limited to any application, but is dependent of staff availability and client required training. The unique automated robotics also enables the Vironomics Core to offer custom and commercial real-time PCR assays to clients.
The Vironomics Core uses several automated robotics for the large-scale real-time PCR. A Tecan Freedom Evo© is used to set up reactions in a 384-well plate, which is then directly run by the synchronised Roche Lightcycler 480 II©. This is a fast and effective way to amplify samples with RT-PCR. Because the Freedom Evo is directly integrated with the Lightcycler, the plates can be run 24 hours/day."

 

In Situ Hybridization Core Facility Provides in situ hybridization services on whole mount as well as cryo and paraffin sections.


Sequencing


The UNC-CH Genome Analysis Facility (formerly the UNC-CH Automated DNA Sequencing Facility) provides researchers at The University of North Carolina at Chapel Hill and external clients with access to state-of-the-art resources for DNA sequencing and genotyping.
Services using Applied Biosystems 3730xl Genetic Analyzers include:
* DNA sequencing in tube format.
* DNA sequencing in plate format (High Thoughput Sequencing).
* Fragment analysis genotyping runs of plates of user prepared samples.
* Sale of limited primers: M13F, M13R and specialty TnA, TnC, TnG, TnX primers.


The High-Throughput Sequencing Facility applies the tools of high throughput sequencing technology to enrich cancer research of UNC scientists.  High throughput sequencing is an extremely fast developing technology, used in many applications such as genome sequencing, genome re-sequencing, chip-seq, cDNA sequencing, digital expression, and microRNA.
The HTSF is a full-service sequencing facility.  The facility offers multiple platforms and several different state-of-the-art techniques to assist with genetic and genomic research.
Platforms available include: Illumina’s Genome Analyyzer II and HiSeq 2000, Ion Torrent and PacBio RS.
Applications include: complete genome re-sequencing (comprehensive polymorphism and mutation discovery in individual genomes) targeted genomic re-sequencing (targeted polymorphism and mutation discovery),
ChIP-seq  (Chromatin immunoprecipitation-sequencing: genome-wide mapping of protein-DNA interactions), small RNA sequencing, transcriptome sequencing (quantification of gene expression and alternative splicing, alternative splicing, transcript annotation, discovery of transcribed SNPs or somatic mutations), sequencing bisulfite-treated DNA and metagenomic sequencing.


Lineberger Comprehensive Cancer Center Genomics Core provides RNA-seq library preparation services for use on Illumina HiSeq 2000 systems.


The Vironomics Core performs next generation sequencing using Roche 454 GS Junior (450 bp read length) and by performing large-scale real time quantitative PCR reactions (please see expression analysis section). The Roche 454 GS Junior sequencing is not limited to any application, but is dependent of staff availability and client required training.


UNC Microbiome Core Facility provides the research community of the UNC- School of Medicine and the state of North Carolina with the facilities and the expertise to characterize complex microbial communities in a variety of environments.
The MCF is equipped to offer the following services: amplicon pyrosequencing, Terminal Restriction Fragment Length Polymorphism (TRFLP) analysis, quantitative (q)-PCR, Clone Library Creation, Consulting and Research Support, including sample genomic DNA isolation, plasmid and virus nucleic acids isolation, RNA isolation, strain typing, optimization of bacterial culture conditions, and high-throughput liquid handling (PCR reaction set up, sample pooling, picogreen quantification of nucleic acids).

 

Genetics


The RNAi Screening Facilityprovides the technology for the UNC scientific community to perform cell based screens and define the contribution of each gene in the human genome to specific phenotypes. RNAi mediated inhibition of gene expression is a powerful method for identifying genes and their cognate phenotype, whose loss of expression alters the cell phenotype. The RNAi HTS Facility manages a human genomic siRNA library from Dharmacon, composed of ~84,500 siRNAs targeting 21,125 genes (Ref Seq database v5.0-8.0).
The facility will provide free-of-charge, the human genome siRNA library, perform the robotic spotting of the library in 384 well microplates, guidance in screen development, support of instrumentation for screen development and implementation of primary and secondary screens. Equipment in the facility includes a Biomek FX for formatting & spotting microplates, BMG Pherastar FS multifunctional plate reader, BioTek liquid drop system (2), Cellomics high-content screening microscope, tissue culture hood and incubators (2), tissue culture microscope, and the ScreenAble software package that provides a high performance toolkit for tracking and analyzing biological screening in microtiter plates.


The Human Pluripotent Stem Cell Core Facilityprovides UNC scientists and outside collaborators with services to successfully conduct basic as well as translational research using human embryonic stem (hES) cells and human induced pluripotent stem (hiPS) cells.
Types of Services & Support Available:
1. Reprogramming human somatic cells to induced pluripotent stem cells
We are using the latest protocols to generate, clonally expand and characterize human induced pluripotent stem (hiPS) cells from a variety of tissue-type fibroblasts. We generate iPS cells using lentiviral transduction and feeder-free conditions and perform quality control experiments to verify the pluripotency of the iPS cells. We are also working on reprogramming peripheral blood cells as well as keratinocytes.
2. Expanding human embryonic stem cell lines
We use the most current protocols to maintain and expand hES cell lines under feeder-free conditions on substrates such as matrigel or fibronectin. For researchers that have purchased human embryonic stem cell lines but do not have the expertise in manipulating these cells, we can thaw, validate, expand and cryopreserve them.
3. Differentiation studies using both hES as well as hiPS cells
We are using current protocols as well as generating new ones to differentiate hES and hiPS cells into a variety of cell types (neuronal progenitor cells, endothelial cells, retinal progenitor cells as well as cardiomyocytes). We are optimizing protocols for hES/hiPS differentiation into mesenchymal, hepatocyte as well as other cell types.


Vector Core facilitates the development of new gene and cell based therapeutics. Our goal is to provide state-of-the-art vectoring technologies and drug product development services at low cost.
The core provides viral and cell-based vectors for both basic and clinical research. The core has low cost production technologies available for all the major viral platforms, as well as technologies to produce custom cell-based products. In addition, the core has established a range of other services designed to support biotherapeutics development research and formal drug development.
Eligible Users include UNC and other academic investigators, as well as government and commercial entities.


Lineberger Comprehensive Cancer Center Genomics Core provides the following services:
1. Measure concentration and check quality for RNA/DNA samples
2. Process samples for Agilent Microarrays (Gene expression, microRNA, and CGH)
3. Prepare mRNA libraries for High Throughput Sequencing

Other Genomics

The Lenti-shRNA Core Facility is premised on Open Biosystems’ TRC1 shRNA libraries. The libraries are cataloged as single lentiviral-vector shRNA expression clones directed to ~16,000 human and mouse genes. Each gene is targeted by 4-5 different shRNAs driven by the U6 promoter. Furthermore, control vectors bearing scrambled shRNAs or shRNAs directed against GFP are available. Please note that the shRNAs’ knockdown efficiency has not been validated. The shRNA core provides lentiviral shRNA vectors in the form of glycerol bacterial stocks or vector particle preparations (~10mL). The shRNA core also provides consulting in designing and optimizing shRNA-encoding lentiviral vectors. Upon request, the core can also provide alternate platforms for shRNA delivery, employing a variety of promoters and other cis elements to improve shRNA expression.

 

Link to Searchable Core Facility database

Back to Categorized Core Listing page