Asuragen’s Affymetrix GeneChip® miRNA Expression Profiling Service

A perfect marriage of miRNA expertise, superior labeling and reliable microarrays

MicroRNA (miRNA) expression profiling, using robust and sensitive microarrays, can provide broad and novel insight into gene regulation. Asuragen’s Affymetrix GeneChip® miRNA profiling service combines Asuragen's miRNA expertise and superior labeling technology with the reliability of Affymetrix microarrays. This service provides our customers with the ability to analyze miRNAs (Sanger 11.0 content) for 71 different species including human, mouse, rat, canine, and monkey with low sample inputs and unparalleled sensitivity. The quality of Affymetrix arrays combined with Asuragen’s stringent quality controls and optimized methods provide high-quality, cost effective solutions for miRNA research, including research on FFPE samples.

Use less of your precious samples while compromising nothing in terms of data quality

Asuragen's proprietary labeling technology requires only 100ng of total RNA for tissues while providing highest miRNA detection and the highest concordance to TaqMan™ data of any labeling methodology. Furthermore, Asuragen has been using this technology for over two years with its proprietary DiscovArray™ miRNA Expression Profiling Service, which is based on an array manufactured by Affymetrix.

Asuragen Labeling performance

General specifications of the Affymetrix GeneChip® miRNA microarrays:

  • Up to 25-mer probe length
  • 4 replicate features per miRNA
  • miRNAs representing 71 species [Probe Content (zip file)]
  • The entire Sanger miRNA database V11.0
  • 900 snoRNAs and 22 ScaRNAs

Learn more about how we qualify our methods and staff.

Performance Specifications of Asuragen Labeling method combined with Affymetrix GeneChip® miRNA Array


Description of Services

Workflow for Affymetrix miRNA profiling services from Asuragen:

  • RNA isolation methods verified to recover miRNA
  • Incoming total RNA QC (sample preparation services):
    • Quantitation and estimation of RNA purity using NanoDrop spectrophotometer readings at 260 and 280 nm
    • qRT-PCR assessment of discrete miRNAs as a surrogate measure of overall miRNA abundance
    • See our Sample Submission and Shipping Instructions for recommended incoming sample QC values
  • Target preparation
  • Array hybridization, washing, and scanning followed by array QC analysis
  • Data summarization (see Deliverables Section)

Deliverables

Included in the price of miRNA expression profiling, you will receive:

  • Affymetrix scanner outputs as DTT and CEL files packaged in a compressed format ready for import into your analysis software
  • Microsoft Excel® workbook containing:
    • Quantile Normalized data using all 71 genomes on the array
    • Sanger 11.0 Annotations for entire array
    • Detection p-values and detection calls

Additional Data Analysis

miRNA Standard Service Premium (miSSP) For statistical analysis and graphical representation of your entire experiment, our miSSP data analysis package offers additional analysis and these deliverables are:

  • Raw Data: CEL Files, DTT file
  • VSN (Variance Stabilization Normalization) Normalized data (default) on selected genome of interest. (Homo sapiens as default)
  • Hypothesis testing with one-way ANOVA or t-Test on selected genome - Statistics include (Means, standard deviation, ANOVA/t-test p-values, LogRatios, Pooled averages; all possible pairwise t-test comparisons (if applicable))
  • Unsupervised clustering: Hierarchical clustering and principal component analysis
  • Publication-quality figures (in JPEG) (some figures may not be included depending on the experimental design):
    • Boxplots (before and after normalization)
    • Heatmap
    • PCA plot
    • Volcano plot
  • Sanger 11.0 Annotations for entire array
  • Detection p-values and detection calls

To ensure security, all information is provided in an electronic form on a DVD. Encryption is available on request. Data may also be delivered by FTP or e-mail.

Quality Control

During our processes, we monitor many QC checkpoints. We utilize in-process sample controls, and process or reagent batch controls. Should any sample-specific QC measure result in an “alert” or “fail” reading, we will contact you to discuss available options. These rigorous procedures enable Asuragen to be the only service provider to offer a Data Quality Guarantee:

  • If, for any reason, a qualified sample does not pass our process control specifications, we will re-run the sample at no additional charge.

Read more about our commitment to the best possible data quality, or read about our contributions to in-process controls and standardization.


Turn-around Time

Most projects are completed in two weeks or less. Contact us if you have a critical time requirement; we can often meet your need for no additional charge. Read more about our commitment to prompt turn-around times.

Additional Services Available from Asuragen


Catalog Numbers for Affymetrix GeneChip Services

CA0032 QC, NanoDrop and TaqMan, Total RNA, for microRNA Applications
CA0096 Target Preparation, Affymetrix miRNA Array, per sample
CA0097 Array Processing and Scanning, Affymetrix GeneChip miRNA Arrays, per sample
CS0010 Data Analysis, per Custom SOW
CS0004 Data analysis, microRNA, SSP, per unit of 100 samples
CC0540 Affymetrix GeneChip® miRNA Array, per sample

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