Agilent Microarrays
Gene Expression
Agilent offers 60-mer oligo microarrays, which are highly sensitive arrays with up-to-date content and coverage. The 60-mer format provides enhancements in sensitivity over 25-mer formats (5-8x more sensitive) partly due to the larger area available for hybridization. Agilent oligo microarrays use only one 60-mer per gene/transcript. 60-mers are also more tolerant of sequence mismatches, which results in simplified analysis of highly polymorphic regions through the use of longer probes.
Custom oligonucleotide-based microarrays can also be purchased through Agilent. Up to 22,000 oligonucleotides per microarray currently can be synthesized for custom arrays. Agilent's inkjet printing format allows for rapid design changes so researchers can tailor the array's design to experimental needs as they change over time.
GSR Microarrays offers microarray services for Agilent's 4 X 44K slide formats, which have four arrays containing 44,000 spots each printed per glass microscope slide. Slides are sold in batches of 5, and with 4 arrays/slide, a minimum purchase yields 20 arrays. Arrays can be used as one-color or two-color and are scanned using GSR Microarrays' GenePix 4000B scanner, which uses GenePix software and generates TIF (image) and .gpr (GenePix Results) files. The .gpr file is a tab-delimited text file that can be opened in Excel and is accepted by the majority of microarray data analysis software. Agilent also offers a software package available for purchase called the Feature Extraction Software. It provides very detailed QC reports on each slide, a text file listing the data values for each feature on each array, an xml file containing data, and other files detailing such things as grid positioning. Most software will import FE data files easily, especially GeneSpring, which is also an Agilent product.
Agilent has recently released an 8 plex format gene expression array for high throughput options for gene expression workflows.
The Agilent SurePrint G3 Human GE 8x60K Microarrays offer the same high sensitivity and accuracy provided by the earlier generation arrays but adds the benefits of extended coverage, greater throughput, and increased cost savings. The new SurePrint G3 Human GE 8x60K Microarrays and Human GE 4x44K v2 Microarrays are based on updated transcriptome databases for mRNA targets, while the SurePrint G3 arrays also include probes for lincRNAs (long intergenic non-coding RNAs). With the combination of mRNA and lincRNAs, it is now possible to perform two experiments on a single microarray, confidently predicting lincRNA function.
miRNA Expression
In addition to the new gene expression arrays, Agilent has also released an miRNA array as an 8plex array format
Agilent microRNA Microarrays generate complete microRNA profiles in order to provide broad insight into expression and regulation. Probe design, coupled with a unique labeling method, works in concert to provide the optimal sensitivity and specificity for miRNA research.
- Content regularly updated from the Sanger miRBase.
- Available in Human, Mouse, Rat, and custom content.
- Optimal sensitivity and specificity through unique probe design method.
- 8x15K slide format printed using Agilent's 60-mer SurePrint technology.
- Each slide contains eight 15K microarrays which can be purchased as a kit of three or as a single slide.
Agilent offerings include standard full genome human, mouse, and rat arrays as well as a large variety of other model organisms including Arabidopsis, C. elegans, yeast, and chicken.
RNA Extraction Recommendation: Total RNA extraction methods differ in numerous ways and may impact the following- yield
- the inclusion of small RNAs in the total RNA extraction
- the quantification of the total RNA
- Absolutely RNA miRNA Kit - Agilent p/n 400814
- miRNeasy Mini Kit - Qiagen p/n 217004
- mirVana RNA Isolation Kit - Applied Biosystem p/n AM1560
- TRIZOL Reagent (100 mL) - Invitrogen p/n 15596-026
When you use these or any other commercial kit, use the total RNA isolation protocol. Do not use the size fractionation or small RNA enrichment protocol.
You must use the same total RNA extraction methods to obtain consistent results for comparative experiments. Different total RNA extraction methods may result in slightly different miRNA profiles. Extraction methods that use organic solvents such as TRIZOL may result in inaccurate quantification, because organic solvent contamination from carry- over during the RNA extraction may compress the 260/230 ratio. The affected 260 measurement may result in inaccurate quantification of the total RNA. If you want to ensure the removal of residual TRIZOL reagent, do one to two additional chloroform extractions after the final extraction step in the TRIZOL protocol, before you continue to the ethanol precipitation.