Leif Oxburgh, DVM, PhD
The Molecular Phenotyping core provides instrumentation, training, and services for in vitro cell phenotyping. Specifically, we provide facilities and training for automated nucleic acids purification, microarray analysis, quantitative PCR, and automated immunofluorescence cell marker analysis and screening.
The core provides access to the following:
- Autogen tissue homogenizer
- Qiagen Qiacube multipurpose DNA/RNA/protein purification system (up to 12 samples)
- Qiagen Qiasymphony automated RNA/DNA prep system
- Nanodrop spectrophotometer
- Caliper Labchip GX nucleic acids separator
- Biorad IQ5 5-channel QPCR instrument
- Biorad CFX384 384-well QPCR instrument
- Biorad MyIQ single-channel QPCR instrument
- Biomek 3000 liquid handler
- Leica DM IRM and Zeiss Axiovert 2 inverted manual epifluorescence microscopes
- Leica DMI6000B with culture chamber for live cell microscopy, microplate screening and automated tiling
- Dell workstations for microarray analysis (X-Ray), statistical analysis (Sigmaplot) and image analysis (Image J, Metamorph)
Core users must be appropriately trained before using core equipment. Please contact Michele Karolak (firstname.lastname@example.org) for instrument training. For workstation training, please contact Leif Oxburgh (email@example.com).
- Qiacube automated RNA/DNA prep system $7.50/run
- Qiasymphony automated RNA/DNA prep system $20/run
- Tissue homogenizer $20/50g Zirconium beads required for run
- Nanodrop spectrophotometer $1/sample
- Caliper Labchip GX nucleic acids separator $3/sample
- Biomek 3000 liquid handler $10/run
- Biorad MyIQ instrument $3.50/hour
- Biorad IQ5 instrument $3.50/hour
- Biorad CFX384 instrument $3.50/hour
- Inverted manual epifluorescence scope $5/hour
- Live cell microscopy/screening $25/day
- Workstation use (microarray, image analysis) $5/hour
The core provides access to workstations running ImageJ for simpler analysis such as pixel counts and particle counts and Metamorph for more demanding procedures such as monolayer cell cycle analysis and image reconstruction.
The core provides access to microarray analysis software. Microarray analyses are performed through a collaboration with the COBRE-supported University of Vermont Medical School Microarray facility.
Genomic scale analyses
With a constantly growing repertoire of annotated genome sequences, it is now feasible to generate sophisticated and highly informative datasets from whole genome comparisons in silico. Such comparisons have been successfully used to identify regulatory sequence associated with specific genes, and have also identified novel regulatory sequence located in gene-poor regions of the genome. For analyses of this scale, we recommend the following resources, all of which are made freely available to academic users. Use of some services may require generating a free account:
NCBI Integrated bioinformatic databases.
MGI Current mouse gene nomenclature with information on gene expression, phenotypes of genetically modified mice and links to available mouse mutants. This is a very useful portal from which to access many other services.
Ensembl Browser for annotated whole genome sequences from a variety of species. Single genes or segments of chromosomes can be downloaded with annotation.
Match Web based service that scans for matches to the Transfac database of transcription factor binding sites within a user-defined query sequence. Multiple parameters can be adjusted in this interface to increase or decrease stringency of matching.
VISTA and rVISTA Tools for cross-species comparisons of genomic sequences. This site also contains pre-computed alignments of whole genomes in which overrepresentation of transcription factor binding sites can be identified within a group of genes, for example genes coregulated in a microarray analysis.
TraFaC Tools for identifying transcription factor binding sites across the whole genome. For example, all genes containing a binding motif for a specific transcription factor within a defined distance from the promoter can be identified. Parameters can be modified to search only regions surrounding the promoter or the entire gene. Furthermore, combinations of transcription factor binding sites can be identified.