Microarray and Gene Expression Core

Contact Lubov Nathanson, Ph. D., lnathanson@med.miami.edu

Copy Number Variance (CNV):
For detection of copy number variants the CGT has purchased Agilent and Nimblegen CGH (Comparative Genome Hybridization), splicing, methylation, and sequencing hybridization platforms.

Gene Expression:

For gene expression studies the CGT possesses two primary platforms: the Affymetrix Gene Chip 3000 and a complete Agilent microarray system.
All forms of expression array, etc. analysis can be supported by these two platforms. In addition, the CGT is capable of supporting, through existing platforms, both Nimblegen and Illumina gene expression studies.

Services provided by Microarray and Gene Expression Core:

• Design of experiments in gene expression, CGH (Comparative Genome Hybridization), Chip-on-chip (chromatin immunoprecipitation), etc. We will determine the optimal design, where with the minimal number of microarrays you will get the most of your results
• Isolation and qualitative assessment of RNA
• Amplification of RNA, if needed
• DNA and amplified RNA labeling
• Hybridization of labeled nucleic acids to Agilent, Nimblegen, Affymetrix or any custom oligo- or cDNA microarrays
• Scanning (resolution up to 5 micron) of any microarrays printed on 1”x 3” slides or Affymetrix arrays
• Image analysis
• Data analysis, which includes (if needed):

• Normalization
• Quality control
• Hit list (list of differentially expressed genes)
• Alternative splicing analysis
• Statistical analysis of replicates (statistically significant changes in expression, calculation of False Discovery Rate, building of linear models and calculation of the interactions between various factors)
• Clustering, PCA, SOM
• Functional analysis (by GO categories, pathway search, protein domain search, etc.)

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