Is there a minimum order requirement for catalog or custom myArray slides?
Yes, we have implemented a minimum order of 5 slides for all myArray products, both catalog and custom arrays.
What equipment will accommodate myArray slides?
myArrays are synthesized on standard sized glass substrates (~26mm x ~75mm x ~1mm). Any equipment (fluidics stations, hybridization stations, scanners, centrifuges, etc.) developed to use standard “microscope” slide-sized substrates should accommodate myArray slides.
Are myArrays made by spotting cDNA?
No. myArrays are made by synthesizing single stranded oliogonucleotides directly on glass substrates.
Are myArrays compatible with Agilent Technologies’ gasket slides and hybridization cassettes?
Yes, myArrays can be used with Agilent Technologies’ gasket slides and hybridization cassettes. Agilent hybridization cassettes are compatible with all myArray formats. Which Agilent gasket slide is used depends on the myArray format. Six by 5K (or 7K) myArrays use Agilent’s 8-gasket backing slide. Three by 15K (or 20K) myArrays use Agilent’s 4-gasket backing slide. Thirty or 40K myArrays use Agilent’s 2-gasket backing slide. All other formats (60, 80K) use a one gasket backing slide.
Does Arbor Biosciences sell hybridization cassettes or backing slides?
No. Agilent Technologies’ hybridization cassettes and backing slides can be found here. If you would prefer other options, please contact techsupport@Mycroarray.com.
Are myArrays compatible with Agilent Technologies’ scanners?
Yes, myArrays can be scanned with an Agilent scanner. However, gal (GenePix alignment) files we provide cannot be used for data extraction. Gal files can be converted to the appropriate Agilent scanner compatible file type but Arbor Biosciences does not support this process. We recommend the Axon 4000 series of scanners.
When I order a myArray, what do I receive?
In addition to your myArray slides, you will receive a spike-in control oligo mixture and, by email, a gal (GenePix alignment) file that describes the location and probe information for each feature. Control oligos may be added to hybridization solution (1l control oligo per 100l of hybridization solution). These fluorescent oligos will bind to control probes on each myArray. Control probes may be omitted upon customer request. Signal from the control probes may help determine if the hybridization and washing stringency were sufficient and aid in proper data extraction grid alignment.
What myArray probe lengths are possible?
myArray probes can be any length the customer desires. However, Arbor Biosciences recommends probes no longer than 50mers. Catalog myArrays have probe lengths of 45-47 bases (the slight variation in probe length insures that all probes fall within a narrow Tm distribution). One myArray may contain probes of different length. Custom probe lengths longer than 50mers are possible (please inquire). Due to the step-wise yield during synthesis (98-99%), it is not advisable or practical to manufacture probes longer than 60mers as the final yield will deteriorate rapidly with longer probes.
In which orientation are probes synthesized?
We synthesize probes 3′ > 5′. This orientation will covalently tether the 3′ end of the probe to a spacer molecule and the 5′ end of the probe will be free.
Are myArrays with removable probes available?
No. All probes on myArrays are not cleavable (removable).
Can probes be synthesized with a free 3' hydroxyl?
Not at this time.
How are the probes attached to the glass substrate?
All probes are synthesized on amine-functionalized glass substrates 3′ > 5′. Probes are covalently attached to the glass substrate as follows: glass-amine-spacer-probe. Probe sequence is pushed away from the substrate surface by first synthesizing a lawn of poly deoxy Thymidine spacer everywhere. The spacer prevents steric hindrance during binding experiments. The default spacer is 15 nucleotides in length. Spacers of different length or composition are available, please inquire.
How do I know which side of the slide has probes?
We use glass substrates that have a notch in one corner for unambiguous orientation. With the notch in the upper right hand corner, as shown in Figure 1, the surface containing probes is facing you. Additionally, the sticky label with bar code will be on the surface that has the probes.
What is the maximum spot density per myArray?
Currently, 80K features per array.
How many myArrays can I get on one glass substrate?
Up to 6 for our standard 5K and 7K formats.
Custom formats are also available. Your custom design, however, must fit within the potential synthesis area.
How many technical replicates should I have of each unique probe sequence?
Catalog arrays have at least three technical replicates of each unique probe sequence within each myArray. Some catalog arrays are available with 5 or more replicates. For custom designs, the extent of probe replication is up to the customer. Different replication levels for different sets of probes can be included on one myArray.
Do custom myArrays cost more?
Because our proprietary synthesis is flexible, often we can synthesize arrays that satisfy customer specifications without increased cost. However, we cannot synthesize features outside of the potential synthesis area (see Figure 1) and the maximum number of features we can synthesize on one slide remains 80K.
Can you synthesize on plastic or on a glass substrate I provide?
We cannot synthesize on plastic. We may be able to synthesize on glass or silicate substrates provided by our customers as long as the substrate dimensions are a standard size (~1mm x ~26mm x ~76mm). In cases where a type of substrate surface modification has not been tested in our system, we recommend a small, low cost, pilot study to determine if oligonucleotide synthesis is possible (based on our QC process) and if your custom myArray functions well in your process.
What size spot can you synthesize?
Our default spot size is ~60mm in diameter. Currently we cannot synthesize spots smaller than the default size. However, we can synthesize features that have a larger surface area compared to the default surface area (~3000mm2). Larger spot sizes will be rectangular. Please contact our technical staff for details.
How are probes designed?
Probes for gene expression myArrays are designed using a proprietary version of publically available software called OligoArray2.1 (see here). Probe sequences for our catalog arrays are deposited in OligoArrayDb (see here
Can custom probes be designed?
Yes. If your organism of interest is not listed on our website, we can design probes for you if the genome has been completely sequenced, fully annotated and publicly available.
Is there a set-up or design fee for a custom probe design?
Typically our standard probe design is complementary. Our standard design attempts to design up to three specific probes per gene. We will likely not be successful for all genes (e.g., some genes will have only 2, 1 or no specific probes). For genes with no specific probes, we may be able to design a probe or probes that are predicted to cross hybridize to other genes. If we include these potentially cross-hybridizing probes on the array (this is up to the customer), we will disclose all “other” genes that may cross hybridize to the probe. Customers may choose the number of specific probes per gene to include on the array (up to 3) and the number of technical replicates per unique probe sequence (minimal recommendation is 3).
Can I submit my own probe sequences?
Yes. Probe sequences are submitted as either a tab delimited text file or an Excel file. Only two columns are necessary; an ID column and a sequence column. Please submit only one instance of each unique probe sequence no matter how many technical replicates you may desire within each array. A third column, replication number, is only necessary if different replication is desired for subsets of probes. Please submit sequences in the standard 5′ > 3′ format. We cannot synthesize degenerate bases (e.g., R, Y, M, K, S, N, etc.), so please submit only A, C, G or T. You may submit probes of any length up to 50 bases.
How do I order myArrays?
Most often customers will request a quote by either contacting sales@ArborBiosciences.com or our myArray product manager, Donald Schwartz, Ph.D. (drs@ArborBiosciences.com). Along with the quote, we will send an order form. To initiate the order, either fill-in and return the order form by email, or have your institution send a PO by email or fax (734)-998-0750.
Is there a discount for bulk orders?
Yes, there are discounts for ordering larger quantities of slides. Currently, there is a 5% discount for ordering 20-49 slides and a 10% discount for ordering 50 or more slides.
What is the typical delivery time?
Most orders are shipped within two weeks of receipt of the order form or PO but it may take up to 4 weeks.
How do I store myArrays?
myArrays are vacuum sealed in a plastic bag inside a plastic slide holder. myArrays are very stabile in the original packaging, assuming the vacuum seal has not been compromised, when stored at the room temperature (~22C) away from moisture and light. Please do not freeze or refrigerate myArrays at any time. Once the slide mailer has been opened, unused slides are best stored in the same mailer and, if possible, stored under vacuum.
How long can myArrays be stored before use?
If stored properly, myArrays should be stabile for at least 6 months.
What temperature should I use during hybridization?
Hybridization temperature depends on a number of variables. Arbor Biosciences technical staff will be able to recommend an initial temperature for your application.
How long should I hybridize?
myArrays are compatible with lifter slips for static hybridizations (incased in a hybridization cassette and immersed in a water bath) and Agilent Technologies gasket slides for dynamic hybridizations (in hybridization ovens using Agilent Technologies hybridization cassettes and backing slides). Typically, >20hrs is recommended for static hybridizations and minimally 12hrs is recommended for dynamic hybridizations. These suggestions assume a fluorescent target concentration of ~35ng/uL, mean length of ~150nt and specific activity of ~1fluor moiety per 30 bases.
Will you provide a recommended hybridization solution recipe?
Yes. We will provide a recommended target preparation and hybridization protocol (for converting total RNA to fluor-coupled amino-allyl-cRNA). The protocol will have a recipe for the hybridization solution.
Washing and Scanning
What equipment do I need to wash myArrays?
myArrays are synthesized on 26mm x 75mm glass substrates. Any washing/hybridization station that accommodates this format should work. However, it is not necessary to have expensive equipment to wash myArrays. Standard 50ml centrifuge tubes can be used, but these can be a bit awkward to use and throughput is poor. Alternatively, standard microscope washing/staining dishes with metal or glass racks can be used. We prefer the later because it is an inexpensive solution, the dishes are readily available from numerous scientific supply houses that sell histology supplies and, with a standard stir plate and stir bar, wash solutions can be agitated to facilitate washing.
Do I need a proprietary scanner to scan myArrays?
No. myArrays are synthesized on 26mm x 75mm glass substrates. Any scanner designed to accommodate ~1×3 inch microscope slides should work well. For example, myArrays have been scanned with the GenePix® 4000B and 4000A (Molecular Devices, Sunnyvale, CA), Agilent, and Innoscan scanners.
What PMT setting should I use for scanning?
Of course the fluorescent intensity of your target as well as the amount of target hybridized impacts the PMT setting. Most scanners will have an option to auto set the PMT, which may or may not work well. We recommend actively adjusting the PMT during scanning so that the full dynamic range of signal is achieved. The PMT should be set such that only a few features (1-2%) have some pixels (<10%) that are saturated. Under these conditions, the full dynamic range of signal intensity is appreciated.
What scanner resolution is needed to scan myArrays?
myArray standard feature diameter is ~60µm. We suggest scanning at 5µm per pixel resolution.