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Microarray Expression and miRNA Profiling

Microarray Expression and miRNA Profiling

Expression & SNP Profiling

Microarray technology for sample screening is a high-throughput method of research that can be used for many applications. Utilizing hundreds of thousands of probes, a microarray can analyze many samples in parallel and generate millions of data points. Microarrays are designed to either detect DNA or RNA through the principles of nucleic acid hybridization.

EpigenDx uses Affymetrix’s GeneChip® arrays to offer services in whole genome SNP genotyping, gene expression, miRNA, cytogenetics, and alternative splicing.

epigendx_Microarray Expression_chart

Featured Microarray Services

Affymetrix Genome-Wide Human SNP Array 6.0

Affymetrix’s high-performance SNP Array 6.0 is EpigenDx’s DNA microarray of choice in Genome-Wide Association Studies (GWAS). Its highly balanced physical coverage and panel power makes it ideal for studying genetic variation. The Genome-Wide Human SNP 6.0 array is Affymetrix’s highest resolution SNP array.


  • 1.8 million genetic markers
    • 906,000 SNPs
    • 946,000 copy number probes
  • Copy Number Variation (CNV) analysis
  • Loss of Heterozygosity (LOH) application

Affymetrix GeneChip®
miRNA 4.0 Array

In recent years, the importance of small non-coding RNAs including microRNA, scaRNA, and snoRNA has risen significantly in the study of epigenetics and expression. The Affymetrix GeneChip® miRNA arrays feature 100% miRBase coverage, and uniquely are capable of independently analyzing pre-miRNA and mature miRNA at the same time.


  • Greater than 15,000 probe sets
  • miRNA, snoRNA, scaRNA, and pre-miRNA in human, mouse, and rat species
  • 100% miRBase coverage (version 15)
  • Coverage in 131 Organisms

Affymetrix CytoScan® HD Array

The CytoScan® High-Density (HD) Array is currently Affymetrix’s highest performance product, with consistent whole-genome coverage (probes at every 250-400 kb interval). Designed for cytogenetic analysis, the CytoScan® HD is an unparalleled platform for applications such as Loss of Heterozygosity (LOH) and Copy Number Variations.


  • 2.6 million markers and probes
  • 750,000 SNPs
  • 1.9 million copy number markers
  • Covers ALL OMIM and RefSeq genes
  • Applications in cytogenetics, LOH, CNV, UPD

Affymetrix GeneChip®
Human U133 Plus 2.0 Array

The Affymetrix GeneChip® Human Genome U133 Plus 2.0 Array is a comprehensive whole genome expression array covering over 47,000 transcripts derived from Genbank™, dbEST, and RefSeq on a single array. It is currently Affymetrix’s most comprehensive whole genome expression array.


  • Analyzes over 47,000 transcripts and variants
  • Coverage in over 38,500 human genes
  • Over 54,000 probe sets and 1.3 million distinct oligonucleotide features

Affymetrix Human Exon 1.0 ST Array

Affymetrix’s GeneChip® Human Exon 1.0 ST Array is designed to provide “exon-level” analysis of genes on a whole-genome scale, to provide a whole-transcript summary of gene expression. Multiple probes on every exon allows the platform to detect alternative splicing and transcript variants, so it is an ideal complement to epigenetics studies.


  • Covers over 1.0 million exon clusters
  • Coverage at 4 probes per exon; 40 probes per gene
  • Applications in gene expression and alternative splicing

The Services Include:

Items Service Products Description Order
8100S-8104g SNP 6.0 Array Sample Analysis Affymetrix SNP 6.0 Array sample analysis service, including:

  • Library Preparation
  • Amplification and Labeling
  • Hybridization/Wash
  • Scanning
Inquiry / Order
8100S-8110a GeneChip® miRNA 4.0 Array Sample Analysis Affymetrix GeneChip® miRNA 4.0 Array sample analysis service, including:

  • Library Preparation
  • Amplification and Labeling
  • Hybridization/Wash
  • Scanning
Inquiry / Order
8100a Microarray Data Analysis Preliminary microarray data analysis using Affymetrix Software and Partket Genomic Suite Inquiry / Order

Ready To Get Started On Your Project?

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