Affymetrix Microarray Gene Expression & SNP Genotyping Service || SeqWright

SeqWright is an Affymetrix® Authorized Service Provider with over 30 years of combined experience involving microarray technologies used in both industry and diagnostic environments. SeqWright's Affymetrix service is GLP-compliant and CLIA certified for handling patient samples.

Download the Microarray ordering form

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 accross 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 coduct global gene expression analysis on their vast archives of small and degragded FFPE samples, using standard affymetrix GeneChip 3' expression arrays.

————————————————————

Common Affymetrix Arrays Include:

Human Genome U133A 2.0	Plasmodium/Anopheles Genome
Mouse Genome 430 2.0	Poplar Genome
Rat Genome 230 2.0	Porcine Genome
Arabidopsis ATH1 Genome	Rhesus Macaque Genome
B. Subtilis Genome (Antisense)	Rice Genome
Barley Genome	S. Aureus Genome
Bovine Genome	Soybean Genome
C. Elegans Genome	Sugar Cane Genome
Canine Genome 2.0	Test3
Chicken Genome	Tomato Genome
Citrus Genome	Vitis Vinifera (grape) Genome
Cotton Genome	Wheat Genome
Drosophila Genome 2.0	Xenopus Laevis Genome
E. Coli Genome 2.0	Xenopus Tropicalis Genome
Maize Genome	Yeast Genome 2.0
Medicago Genome	Yeast Genome S98
P. Aeruginosa Genome	Zebrafish Genome

See Affymetrix's Website for the Complete List of Arrays

————————————————————

Genome-Wide Methylation Analysis on an Affy 100K Chip

SeqWright offers genome-wide scans for detecting hyper/hypo-methylation on the Affymetrix Human 100K mapping set. Our proprietary technique takes advantage of certain methylation-sensitive enzymes combined with a novel screening and detection technology. Targeted identification and validation of methylated CpGs is performed using DNA sequencing.

SNP Genotyping

GLP-level SNP genotpying can be performed on the Affymetrix Genome-wide Human SNP array 5.0 and 6.0 or on the Affymetrix 100K and 500K mapping sets. We also offer a canine genotyping array, developed by the Broad Institute at M.I.T. As little as 250 ng of gDNA is needed per array. Applications for this service include:

•	Chromosome Copy Number Analysis
•	Whole-Genome Association Studies
•	Cancer Genetics
•	Linkage Disequilibrium
•	Case Control
•	Family-Based Association Studies