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 platform 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 ServicesDeliverables
Quality Control
Turn-around Time
Data Analysis
Additional Services Available
Available Sentrix® BeadChips
Catalog Numbers for Affymetrix Services
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)
- 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 (click here for additional analysis services)
Sample Submission Form and Shipping Instructions
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 many 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 two weeks or less. 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.
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.
Mouse-6 Expression BeadChips
The Mouse-6 BeadChip enables the profiling of more than 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 Sentrix Human-6 v2 Array* |
| CC0170 | Illumina Ratref-12 Expression Beadchip* |
| CC0180 | Illumina Mouse-6 Expression Beadchip* |
| CA0051 | Array processing and scanning, DASL |
| CA0055 | Target preparation, DASL |
| CC0220 | Illumina Sentrix 96 Array Matrix, DASL |
*Asuragen supports a broad range of arrays from Illumina. Contact Asuragen for more detail.