Illumina Gene Expression Profiling

Asuragen is proud to be the first commercial service provider in the world to offer gene expression profiling on the Illumina platform. Low sample input requirements and cost-effective platforms coupled with our validated procedures and optimized workflow processes give you the confidence and turn-around time critical for a successful experiment. Learn more about how we qualify our methods and staff.

Description of Services

Workflow for gene expression services:

  • Incoming total RNA QC (click here for sample prep services):
    • Quantitation and estimation of RNA purity using NanoDrop spectrophotometer readings at 260 and 280 nm
    • Assessment of RNA integrity using Agilent 2100 Bioanalyzer to measure RNA integrity number (RIN) for RNA prepared by Asuragen (not applicable for FFPE samples)
    • For Illumina DASL: qRT-PCR assessment of housekeeping genes as a surrogate measure of overall mRNA abundance
    • See our Sample Submission Form and Shipping Instructions for recommended incoming sample QC values
  • Target preparation utilizing the Illumina-recommended single-round amplification process. The process consists of reverse transcription (RT), second strand cDNA synthesis, and IVT cRNA generation (eukaryotic only) followed by cRNA QC
  • Array hybridization, washing, and scanning followed by array QC
  • Data summarization (additional analysis services)

Deliverables

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

  • Illumina Scanner outputs for BeadChip arrays including IDAT, JPG, and SDF files
  • Microsoft Excel® workbook containing:
    • Gene Identifiers
    • Summarization of RNA QC values
    • Summarization of gene values using Illumina BeadStudio Software
    • Illumina Array QC report derived from quality metrics set by Asuragen
  • Agilent Bioanalyzer RNA QC report in PDF format

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 QC checkpoints as recommended by the Illumina BeadChip procedures. As much as possible, we utilize spike-in controls, 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 one to two weeks. 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.

Data Analysis

Asuragen’s Bioinformatics team is very experienced with whole genome expression analysis. As part of the Standard Service for gene expression profiling, our team summarizes the data and provides you with a report that outlines each step of the analysis project and presents your findings so that you can advance to the next stage of investigation and experimentation.

Additional Data Analysis

Standard Service Premium (SSP)

For statistical analysis and graphical representation of your entire experiment, our SSP data analysis package offers additional analysis and these deliverables:

  • Hypothesis testing by one- or multi-way ANOVA of the summarized array data, providing p-value and fold-change information relevant to your experimental groups
  • Publication-quality figures and images, including:
    • Hierarchical clustering
    • Pair-wise volcano plot(s)
    • Box plot(s)
    • Principal components analysis (PCA) plot(s)

These are provided in electronic form on the data delivery DVD in addition to the standard deliverables provided with every gene expression profiling project.

In addition, with all SSP projects we will call you upon shipment of your data to arrange a one-hour web-based informatics review of your data.

Full Service

Based on your initial consultation, Asuragen can define expert analysis for a custom informatics approach.  See our Informatics section for more information on our capabilities.

Additional Services Available

Available Sentrix® BeadChips

Human-6 Expression BeadChips The Human-6 BeadChip enables the generation of whole-genome expression profiles with > 47,000 probes targeting > 46,000 human transcripts. Each array on the Human-6 BeadChip provides genome-wide transcriptional coverage of well-characterized genes, gene candidates, and splice variants.

Human HT-12 Expression BeadChips Content is identical to Human whole-genome 6 BeadChip, but with an average 15-fold redundancy instead of 30-fold. This chip is the highest throughput whole-genome expression BeadChip.

Mouse-6 Expression BeadChips The Mouse-6 BeadChip enables the profiling of > 47,000 transcripts. BeadChip content was created by combining proven sources, including the MEEBO set, the RIKEN® FANTOM 2 database and the NCBI RefSeq database.

RatRef-12 Expression BeadChips The RatRef-12 BeadChip contains > 22,000 probes based on the NCBI RefSeq database (release 16).

DASL® for FFPE
Gene expression solution designed to generate reproducible profiles from degraded RNAs such as those derived from formalin-fixed, paraffin-embedded (FFPE) tissues.

Asuragen also supports additional Illumina products on a custom basis. Please inquire

Catalog Numbers for Gene Expression Services

CA0010 QC, NanoDrop and Bioanalyzer, Total RNA, for mRNA applications
CA0034 Target Preparation, cRNA, Illumina Standard Input with QC
CA0038 Array Processing and Scanning, Illumina Arrays
CC0150 Illumina Human-6 v2 Array*
CC0170 Illumina Ratref-12 Expression Beadchip*
CC0180 Illumina Mouse-6 Expression Beadchip*
CA0051 Array processing and scanning, Illumina DASL Array
CA0055 Target preparation, Illumina DASL Array
CC0220 Illumina Sentrix Universal 96 Array Matrix, DASL
CC0330 Illumina Human HT-12 Array, for 12 samples

Select your region

Map of the world

Select your region below to learn more about Asuragen’s technology and scientific expertise as well as information about products available in your region.