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Expression Profiling
Please contact SeqWright before sending samples for any study. Consultations are no charge. Below is some important information regarding of our core microarray expression profiling service:
- Starting Material: Blood, Cells, Tissue, Total RNA, and mRNA
- QC on an Agilent 2100 Bioanalyzer RNA LabChip
- Concentration determined by a NanoDrop® ND-1000
- Available 2-cycle target labeling assays for low quantities of RNA
- Array hybridization on any of the available chips through Affymetrix
- Affymetrix GSC3000 4-color scanning
- Image capture and data extraction
- Comprehensive statistical analysis across any number set of patients
- GLP compliant
- 5 day turnaround on most projects
Analyses of Expression Microarray Data
- Computation of a global normalized expression metric using Robust Multiarray Average (RMA) of the hybridization intensity data from all chips in the experimental set
(Probe annotations will be added at this step.)
- QC Analysis:
Histograms for PM intensity data
Pattern of 5’-3’ probe RNA degradation
- Experiments with 2 conditions:
Analysis of the pattern of expressed and non-expressed transcripts with screening of genes for later analyses
Parametric (t-test) or nonparametric (Mann-Whitney U-test) for significant differences in patterns of expression between groups
Within-gene permutation testing for empirical significance with and without randomization
- Experiments with 3 or more conditions
Analysis of the pattern of expressed and non-expressed transcripts with screening of genes for later analyses
Parametric F-test (ANOVA) or non-parametric (Kruskal-Wallis) for significant differences in patterns of expression between groups
Within-gene permutation testing for empirical significance with and without randomization
- Computation of Positive False Discovery Rate (pFDR) statistics using Storey q-value
- Exploratory Data Analysis
K-means cluster analysis using agglomeration and distance measures to search for patterns of sample and/or transcript clustering - production of corresponding heatmap
Other exploratory data methods available – Principal Components, Factor Analysis, Linear Discriminant Analysis, Cannonical Discriminant Analysis
SeqWright can now perform Expression Analysis on your FFPE (formalin-fixed, paraffin-embedded) Samples!
Using NuGEN's WT-Ovation System®, we can provide scientists the opportunity to conduct global gene expression analysis on their vast archives of small and degraded FFPE samples, using standard Affymetrix GeneChip 3' expression arrays.
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