Illumina Platform
With 100% array quality control, high feature redundancy, multi-sample array formats,
and built in flexibility, the Illumina platforms provide a cost-effective, novel
approach to expression profiling. Asuragen was the first Certified Service Provider
(CSP) for Gene Expression analysis on the Illumina platform.
Services Available
Technology
Sentrix® BeadChip for Gene Expression
Uniform pits are etched into the surface of each substrate (to a depth of approximately
3 microns) prior to assembly. The BeadChip format uses a planar silica substrate
in a slide format coated with a photo-resistant substance before plasma etching,
followed by cleaning, to reveal uniformly etched wells. Beads are then randomly
assembled and held in these micro-wells by Van der Waals forces and hydrostatic
interactions with the walls of the well. Learn more
BeadArray Manufacturing Process
Individual bead types are created in manufacturing lots of several million. Full-length
oligos are coupled to beads through an amine linkage, creating a “bead type” for
each bead + oligo combination. Bead types are pooled together to form assay panels
for as few as 96 or as many as 650,000.
BeadArray Technology Advantages This novel approach to microarrays has a number
of advantages, including:
- 100% Array Quality Control: The manufacturing process includes
a functional validation (by sequential hybridization) of every single array element
(bead with oligos). This process, called decoding, allows Illumina to QC every feature
of every array to ensure that each array element is present and functional
- High Redundancy: Each element is represented in high redundancy
(> 20-fold), providing industry-leading data quality and reproducibility, through
comparison and averaging of the many beads of the same type in an experiment
- Flexibility: New bead pools are easily synthesized and deployed
onto either of two substrates, providing rapid availability of new products and
fast turnaround for custom panels
DASL Assay Technology
The cDNA-mediated Annealing, Selection, Extension, and Ligation (DASL) Assay allows
for RNA profiling of up to 1,536 targets using partially degraded RNA as found in
formalin-fixed, paraffin-embedded (FFPE) samples. Using either the Universal-16
or the Universal-96 choice Array Matrix format for sample processing, the DASL Assay
offers researchers the opportunity to analyze hundreds to thousands of RNA transcripts
derived from previously collected, preserved samples. The DASL Assay leverages the
proven GoldenGate Assay protocol to provide high-quality data for an RNA-based application.
Because the probe groups span only about 50 bases, partially degraded RNA can be
used in the assay. The availability of additional, unique probe sequences per gene
increases the sensitivity of the assay, allowing the quantitation of low-abundance
transcripts, even in partially degraded samples.
DASL assay highlights
- Reproducible RNA profiling: Profile partially-degraded RNAs such
as those found in formalin-fixed, paraffin-embedded (FFPE)
samples
- Proven sensitivity: Detect low-abundance transcripts
- Ideal for clinical sample types: Requires an input of just 100–200
ng total RNA
- Flexible formats: Process in groups of 16 or 96 samples
Quality Control
Proficiency testing of Asuragen’s processes and operations consisted of duplication
of the PowerAssist™ analysis of the MAQC reference samples. This assures you that
our sensitivity and technical reproducibility are comparable to the Illumina results
published in the MAQC.
No matter how robust the downstream processes, good data is dependent on sample
quality; consequently, accurate measurement of sample quality is essential before
deciding if a sample merits further analysis. All samples prepared by Asuragen Services
are routinely qualified by spectrophotometry with the
NanoDrop spectrophotometer and the
Agilent 2100 Bioanalyzer.
Due to the degraded nature of RNA from FFPE tissues, special quality control measurements
are used in place of the Bioanalyzer.
Regardless of downstream application, detailed QC reports including nucleic acid
concentration, RNA integrity (RIN),
electropherograms (where applicable), and purity are provided on each sample. For
FFPE samples, concentration and QC pass/fail information is provided. If a sample
does not pass a recommended QC metric for analysis, you will be contacted promptly
to discuss possible solutions. These may include replacing the sample or re-isolating
the RNA, excluding the sample from further analysis, or proceeding at-risk.
Yield:
RNA yield is primarily dependent on the tissue type and mass (or volume) but is
often affected by disease status, chemical treatment, media, preservatives, and
tissue handling.
Integrity:
RNA integrity is dependent on a wide range of factors in the precise handling of
biological materials from collection to RNA isolation. Elimination of the activity
of endogenous endo- or exo-nucleases is vital to preserving RNA integrity, and typically
depends on treatment with proper preservative or freezing upon tissue collection.
Asuragen’s 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.
Sample Handling and Processing
All samples are received and entered into the analysis queue under a controlled
SOP to confirm package/sample integrity, appropriate shipping conditions (frozen
samples/dry ice, as appropriate), and individual confirmation of sample identity
against the shipping manifest and electronic sample
submission form and
instructions.
Turn-around Time
Typical turn-around time is 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.
Related Services
Data Analysis
Asuragen’s Informatics Team
offers a broad range of analytical services to help you get the most information
from your data.
Catalog Numbers for Illumina Services
Gene Expression
|
CA0010
|
QC, Nanodrop and Bioanalyzer, Total RNA, for mRNA Applications
|
|
CA0034
|
Target Preparation, cRNA, Illumina Standard Input with QC
|
|
CA0067
|
Target Preparation, cRNA, Illumina HT-12 with QC
|
|
CA0038
|
Array Processing and Scanning, Illumina Arrays
|
Gene Expression Data Analysis
|
CS0001
|
Fee, Initial Consult or Design Plan
|
|
CS0002
|
Data Analysis, mRNA, Standard Service Premium
|
|
CS0003
|
Fee, Setup
|
DASL Gene Expression for FFPE
|
CA0037
|
QC, NanoDrop and TaqMan, Total RNA, for mRNA Applications
|
|
CA0055
|
Target Preparation, Illumina DASL
|
|
CA0051
|
Array Processing and Scanning, Ilumina DASL Arrays
|
|
CC0220
|
Illumina DASL Sentrix Universal 96 Array Matrix, for 96 samples
|
|
CC0230
|
Illumina DASL Sentrix Unversal Beadchip, for 16 samples
|
*Asuragen supports a broad range of arrays from Illumina.
Contact Asuragen for more detail.
How does Illumina compare to the Affymetrix platform?
The Illumina platform was analyzed as part of the MicroArray Quality Control (MAQC)
Project. A high level of interplatform concordance was observed in the results produced
by Illumina BeadChips and Affymetrix GeneChips.
Learn more about the MAQC project