Frequently Asked Questions

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FAQ: OneArray® Microarray Products and Services

  1.) How many probes does each OneArray® product contain?
2.) Where can I obtain the OneArray® probe sequences?
3.) How are OneArray® microarrays manufactured? Why does this provide superior quality?
4.) What can I do if I am unsatisfied with your product?
5.) How sensitive is OneArray®? How reproducible is OneArray®
6.) Do you offer hybridization services? 
7.) What do I need to start using OneArray®?
8.) Is OneArray® customizable?
9.) How do I properly store OneArray® microarrays?
10.) How long does the warranty for OneArray® products last?
11.) Can I reuse OneArray® microarrays?
12.) What scanners are compatible with OneArray® microarrays?
13.) Which fluorescent dyes are used with OneArray®?
14.) Where can I find the most up-to-date User Guide for my OneArray® product?
15.) How much target sample do I need to use with OneArray®? How do I quantify my target?
16.) How do I prepare my target sample for hybridization? 
17.) How do I purify my cDNA sample to remove any traces of free dye? 
18.) How do I prepare my OneArray® microarray for hybridization? 
19.) I am accustomed to a different hybridization protocol and buffer; can I use them with OneArray®?
20.) Which side of the slide contains the probes? 
21.) What data analysis packages are available? 
22.) How do I evaluate the experimental control probes embedded in OneArray®
23.) I have identified a relevant feature: what is the gene?

1.) How many probes does each OneArray® product contain?
To provide customers with relevant expression assays, our microarrays are periodically reprinted with the latest probe content. Also, the annotation for the probes are frequently updated to provide relevant information. The overall probe information can be found under the product page. The details of each probe set are described within the respective product pages, and full annotations can be found under technical support - gene lists.

2.) Where can I obtain the OneArray® probe sequences?     
The probe sequences are freely available on the OneArray Website here.

3.) How are OneArray® microarrays manufactured? Why does this provide superior quality?         
OneArray® microarrays are manufactured using non-contact Thermo Jet technology that generates highly reproducible microarrays with unmatched intraspot homogeneity. The special printing process allows probes to immobilize on the array evenly, providing higher quality data for analysis. For more information, visit the OneArray Web site here.

4.) What can I do if I am unsatisfied with your product?
All OneArray products and services are backed by a 100% satisfaction guarantee. If you are unsatisfied for any reason, please contact us at 650-320-8669 for a replacement or refund.

5.) How sensitive is OneArray®? How reproducible is OneArray®?   
OneArray is sensitive to 0.05 picomolar over a range of 2-3 orders of magnitude. Array-to-array reproducibility is >98% for both Human and Mouse OneArrays.

6.) Do you offer hybridization services?      
Yes. Our hybridization services are designed for the laboratory that is not equipped with instruments and/or personnel to perform microarray experiments. Several options are available for labeling methods, dyes, and amplification. OneArray microarray experts are available to assist you with defining starting material requirements, experimental design specifications, determination of cost and completion schedule. To get your project started, contact us at:

7.) What do I need to start using OneArray®?
The following materials are necessary to use the OneArray® microarrays:

Necessary Apparatus & Reagents (Not Supplied)

Apparatus
- Water bath/heating block
- Hybridization oven
- Powder-free gloves
- Hybridization accessories: chamber cover slides, etc.
- Rectangular slide staining dish and slide rack for washing microarrays
- Micropipettors
- PCR (polymerase chain reaction) machine
- Sterilized and nuclease-free pipet tips
- Microarray scanner for standard 1” x 3” standard format slides
- Sterilized and nuclease-free microcentrifuge tubes
- Hybridization systems (optional)
- Microcentrifuge
- Clips and Clean, blunt forceps
- Automated hybridization station (optional)

Reagents
- De-ionized nuclease-free water
- De-ionized formamide
- Cyanine 3- or Cyanine 5-labeled amplified aRNA sample; or Cyanine 3- or Cyanine 5-labeled cDNA sample
- BSA (bovine serum albumin)
NOTE: BSA must be molecular-tested

Alternatives to Salmon Sperm DNA Blocking Mixtures:
- Ambion® Sheared Salmon Sperm DNA (10 mg/ml), or
- Invitrogen™ Cot-1 DNA® (2.5 10 mg/ml), or
- Invitrogen™ Poly-A (2.5 10 mg/ml)

Wash solutions (four types, all necessary):
- 2X SSPE, 0.1% SDS solution
- 2X SSPE
- 0.1X SSPE, 0.1% SDS solution
- 0.1X SSPE

8.) Is OneArray® customizable?
Yes. Our skilled scientists will work with you to provide custom microarrays with the same exceptional quality as our OneArray® microarrays. To contact one of our scientists, send an e-mail message to:

9.) How do I properly store OneArray® microarrays?
Your microarrays should be stored unopened at 4°C. Once opened, microarrays should be used within one week. The accompanying storage buffer should be stored at room temperature.

10.) How long does the warranty for OneArray® products last?
We guarantee the performance of OneArray® for 12 months.

11.) Can I reuse OneArray® microarrays?
No. OneArray® microarrays are designed for single-use only.

12.) What scanners are compatible with OneArray® microarrays?
The following is a partial list of scanners that are compatible with OneArray microarrays:

  Compatible Microarray Scanners
 
Manufacturer Product Name and Description
Molecular Devices GenePix® 4000 A/B
Genomic Solutions,® Inc. GeneTac™ 2000
Perkin Elmer, ® Inc. Scan Array™  5000
TECAN® LS 200/300/400
Agilent Technology DNA Microarray Scanner G2565B
  NOTE: The performance of different makes and models of scanners can vary, therefore, it is recommended that the scanner used be sufficiently tested and adjusted for use with the OneArray DNA Microarray based on standard microarray calibration parameters.

13.) Which fluorescent dyes are used with OneArray®?
OneArray microarrays contain experimental control probes with Cy3 and Cy5 dyes. In order to properly utilize the control probes, your scanner should be set to measure signal from these dyes.

14.) Where can I find the most up-to-date User Guide for my OneArray® product?
Our Web site always has the most current version of all User Guides and other documentation. To obtain documentation, please visit our Support Page .

15.) How much target sample do I need to use with OneArray®? How do I quantify my target?
High quality, intact RNA is essential for all gene expression microarray experiments. We recommend that you start with at least 2µg labeled target RNA for cover-slip hybridization. However, some hybridization systems provide more efficiency. Please refer to the manufacturer’s instructions.

To quantify using UV absorbance, an A260 of 1 is equivalent to 40 µg RNA/ml. A convenient instrument for this analysis that requires no dilution or cuvettes is the NanoDrop® spectrophotometer. To quantify using RiboGreen® (Molecular Probes) please refer to the manufacturer’s instructions.

16.) How do I prepare my target sample for hybridization?    
Target samples can be prepared using a variety of commercially available kits. Select a labeling kit or protocol that is most suitable for your specific needs. The following kits have been tested and are known to be compatible with OneArray® microarrays:

aRNA Preparation:
For preparation of amino allyl aRNA suitable for indirect labeling:
- Amino Allyl MessageAmp II™ aRNA kit by Ambion

For pre-hybridization fragmentation of aRNA:
- aRNA Fragmentation Reagent by Ambion

For preparation of aRNA via T7 incorporation of modified nucleotides (direct labeling):
- MessageAmp™ aRNA Amplification Kit by Ambion

cDNA Preparation:
For cDNA preparation suitable for indirect labeling:
- Amino Allyl MessageAmp II™ cDNA kit by Ambion
- Superscript Indirect Labeling System by Invitrogen
- Fairplay II Microarray Labeling Kit by Stratagene™

For preparation of cDNA via RT incorporation of modified nucleotides (direct labeling):
- MessageAmp™ aRNA Amplification Kit by Ambion

17.) How do I purify my cDNA sample to remove any traces of free dye?       
It is strongly recommended that you re-purify your targets with Qiagen Mini-Elute PCR purification columns. Failure to do so may cause high background signal intensity and result in lower quality data.

18.) How do I prepare my OneArray® microarray for hybridization? 
It is vital that the pre-hybridization protocol is carefully followed to prepare OneArray® microarrays for hybridization. See the OneArray® User Guide for detailed instructions. Failure to properly complete the pre-hybridization protocol may cause high background signal intensity and result in lower quality data.

19.) I am accustomed to a different hybridization protocol and buffer; can I use them with OneArray®?
OneArray microarrays have been optimized for use with the supplied Hybridization Buffer and accompanying protocol. However, you may have a specific application that requires different conditions. We recommend that you consult with one of our scientists to ensure your protocol is compatible with the OneArray® microarray.

20.) Which side of the slide contains the probes?       
The probes are spotted onto the same side as the bar code.

21.) What data analysis packages are available?       
There are a variety of academic and commercial data analysis packages available that are compatible with OneArray microarrays. A partial list follows.

  Compatible Data Analysis Packages
 
Organization Product Name
Washington University in St. Louis Dapple
National Institutes of Health F-scan
Lawrence Berkeley National Lab ScanAlyze
The Institute for Genomic Research Spotfinder
University of California, San Francisco UCSF Spot
Molecular Devices (previously Axon Instruments) GenePix Pro
BioDiscovery ImaGene
MediaCybernetics Array Pro
Imaging Research, Inc. ArrayVision

22.) How do I evaluate the experimental control probes embedded in OneArray®
The control probes can be easily analyzed using the software program, SimpleMeasure™ 1.4, a compact Java applet that is freely available on our Web site here.

We recommend downloading and reading the Simple Measure 1.4 User Guide before installing the program.
NOTE: The OneArray® User Guide contains the information necessary to evaluate all the data generated by SimpleMeasure™ 1.4.

23.) I have identified a relevant feature: what is the gene?
Our Web site contains the most up-to-date versions of OneArray® microarray annotations. Please access our Support page.
For each microarray, there are the following files:
- Probe Annotation File (*.paf): the Ensembl ID and description of the corresponding gene’s function.
- General Feature Format (*.gff): the genomic coordinate file.
These annotation files are updated regularly with every release of the Ensembl database—approximately every two months.