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GeneChip® miRNA Array

The GeneChip® miRNA Array is a powerful tool for studying the role of microRNAs (miRNAs) and their importance in cancer and other diseases. In addition, miRNA studies facilitate the discovery of biomarkers and disease signatures.

Non-coding RNAs are emerging as a major component of the regulatory circuitry that underlies the development and physiology of complex organisms. miRNAs are small, single-stranded RNAs that regulate gene expression by partial complementary base pairing to specific mRNAs. This annealing inhibits protein translation and in some cases facilitates the degradation of mRNA.

The GeneChip miRNA Array also includes human small nucleolar RNAs (snoRNAs and scaRNAs), which are short, non-translated RNAs that play a role in processing of ribosomal RNAs following transcription. snoRNAs have also been implicated in the regulation of alternative splicing.

Affymetrix Solution

GeneChip® miRNA Array

  • The most comprehensive miRNA coverage with multiple organisms on a single array
    • Human, mouse, rat, canine, and monkey - all important species for research and pharmaceutical drug development
    • Sanger miRNA database V11 content and additional human small nuclear RNAs (snoRNAs and scaRNAs)
  • miRNA profiling on the industry's most reliable microarray platform
    • Arrays are synthesized using Affymetrix' high-quality photolithography process to ensure optimal performance
    • Contains controls to ensure success of your experiment
  • Investment leverage
    • Leverage your existing Affymetrix instrument - cost savings and convenience

miRNA QC Tool

Free miRNA QC Tool for data summarization, normalization and quality control. A new version ( is now available.

Genisphere® Solution

FlashTag™ Biotin RNA Labeling Kits for use with Affymetrix® miRNA Arrays:

  • Reproducibility: CVs ≤ 10%
  • Sensitivity: ≤ 10 attomoles
  • Dynamic Range: 4 log10
  • Specificity: 1 nucleotide discrimination
  • Rapid, 45 minute Labeling of Total RNA
  • In-Process Labeling QC Assay
  • Low input amounts: 0.1 - 3µg total RNA



FlashTag™ Biotin HSR RNA Labeling Kit (pdf, 217 KB)

miRNA Arrays (pdf, 1.85 MB)


Expression Console™ Software (pdf, 6 MB)

Expression microarray reagent guide (121 KB)

Expression Wash, Stain and Scan User Manual for Cartridge Arrays (pdf, 2.52 MB)

FlashTag™ Biotin HSR RNA Labeling Kit for GeneChip® miRNA Arrays (pdf, 597 KB)

Sample Attribute Editor (pdf, 597 KB)

Transcriptome Analysis Console (pdf, 7 MB)

User Guide, GeneChip® miRNA 2.0 Assay Software Module (pdf, 876 KB)

Quick Reference Cards

Expression Console Quick Reference Card (pdf, 1.13 MB)

Sample Data

miRNA 2.0 Sample Data (zip, 5.75 MB)

miRNA 3.0 Sample Data (zip, 4.96 MB)

miRNA 4.0 Sample Data (zip, 4.3 MB)

miRNA Array Sample Data (zip, 708 KB)

Library Files

GeneChip® miRNA Array 3.0 TAC Configuration File

GeneChip® miRNA Array 4.0 TAC Configuration File

Installing GeneChip miRNA 3.0 Array Library Files for AGCC

miRNA 2.0 AGCC Library File Installer

miRNA 2.0 Analysis Files for Expression Console

miRNA 3.0 AGCC Library File Installer

miRNA 3.0 Analysis Files for Expression Console

miRNA 3.0 CDF Library File (zip, 4 MB)

miRNA 4.0 AGCC Library File Installer

miRNA 4.0 Analysis Files for Expression Console

miRNA 4.0 CDF Library File (zip, 5 MB)

Package Inserts

miRNA 2.0 Array (pdf, 124 KB)

miRNA 3.0 Array (pdf, 159 KB)

miRNA 4.0 Array (pdf, 159 KB)

miRNA Array (pdf, 520 KB)

miRNA Array Plate Package Insert (pdf, 180 KB)

miRNA Array Strip Package Insert (pdf 82 KB)

Alignment, Annotation, and Sequence Files

Information about using Alignment, Annotation, and Sequence files

Current NetAffx Annotation Files

miRNA-2_0 Annotations, CSV format (533 KB, 3/13/12)

miRNA-3_0 Annotations, CSV format (21 MB, 5/13/14)

miRNA-4_0 Annotations, CSV format (23 MB, 10/3/16)

Note: NetAffx annotation files are intended for use in automated analysis. Some are not compatible with all spreadsheet applications. Please use the NetAffx Analysis Center to limit download data to your probe sets of interest. Annotation CSV files for the exon arrays are split into a probe set-level annotation file and a transcript cluster-level annotation file; exon array CSV files are compatible with ExACT.

Additional Support

Annotations, Unsupported, 20160617 CSV format (25 MB)

miRNA 1.0 Annotations, Unsupported, CSV format (zip, 213 KB)

miRNA 3.0 probe list (zip, 3.79 MB)

Probe List, Unsupported, TXT format

Species Lookup Table (zip, 1.33 MB)

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Part # Description Details
901324 GeneChip® miRNA Array Contains 2 Arrays
901325 GeneChip® miRNA Array Contains 6 Arrays
901326 GeneChip® miRNA Array Contains 30 Arrays

Required Products

Part # Description Details
Affymetrix® GeneChip® Command Console® Software (AGCC)
00-0079 GeneChip® Fluidics Station 450

Related Products

Part # Description Details
900301 Control Oligo B2 (included in Hybridization Control Kit) Sufficient for 30 reactions
900720 GeneChip® Hybridization, Wash and Stain Kit Sufficient for 30 reactions
900454 GeneChip® Hybridization Control Kit Sufficient for 30 reactions
900721 Wash Buffer A 800 mL
900722 Wash Buffer B 600 mL
FT10AFYB Genisphere FlashTagTM Biotin RNA Labeling Kits for use with Affymetrix miRNA Arrays Sufficient for 10 reactions
FT30AFYB Genisphere FlashTagTM Biotin RNA Labeling Kits for use with Affymetrix miRNA Arrays Sufficient for 30 reactions