1. GENERAL QUESTIONS:

  • What factors are considered when making a price quote?  EcoArray considers the experimental design of a unique project when giving a price quote to a customer.  Pricing depends on, among other things, how much sample preparation will be done at EcoArray, the type and number of samples, the species of interest, the number of genes to be sequenced or arrays to be run, and who does the analysis.  Quotes for some of our products and services are available online. It is our policy to provide academic/government discounts and volume (quantity) discounts, and when applicable.  If you are interested in the FHMinnow arrays, we have special pricing for those willing to put data in our database. We encourage all potential customers to contact us before purchase to get the best price available.

  • If I was given an academic/government discount, what did I agree to do? It is EcoArray’s policy to provide academic/government discounts to eligible customers provided they agree to the following terms and conditions:

ACADEMIC/GOVERNMENT PRICING TERMS AND CONDITIONS

    • The products and services will be used for research purposes only and cannot be resold.  If any products or services that are developed or sold by EcoArray become part of a commercial product, the seller of such commercial product must license such technology from EcoArray.
    • If the work associated with the products and services results in publications, EcoArray expects to be acknowledged in the publications.

  • What are the conditions for commercial pricing? 

COMMERCIAL PRICING TERMS AND CONDITIONS

    • The customer owns all products, services, and associated intellectual property.
    • All products developed during the service contract will be shipped back to the customer unless otherwise specified.
    • If the work associated with the products and services results in publications, EcoArray expects to be acknowledged in the publications.

  • Will EcoArray provide training to me?   EcoArray does not provide training at this time on any of our services.  Customers who purchase arrays (nylon membrane or glass slide) to run in their own lab also receive our recommended protocols for processing the arrays. Should you have questions about the protocols or any other products and services, EcoArray expects to answer them.  Please contact us.  We may consider conducting array hybridization training workshops in the future if there is enough interest.  In the meantime, Agilent offers training sessions and extensive web support for processing their oligonucleotide microarrays. 
  • What technical support may I expect? EcoArray technicians will answer questions related to our technology. For oligonucleotide microarrays, we will often direct you to Agilent. You may contact us by email or phone. 
  • How can a for-profit company be more cost effective for me than an academic lab?  Cost is just one of the variables that must be considered when a project is formulated.  Generally, the institution underwrites the academic labs so salaries, rent, and other factors that go into a company’s “overhead” do not have to be recovered.  This means that academic labs often can charge a customer a lower price for the same service that is offered commercially.  However, for-profit companies may provide a faster turn-around time, better quality guarantees, and may even have more experience with your particular type project.  If factors other than price are important, it may be cost effective to use a commercial company rather than an academic lab. 
  • How much experience does EcoArray have with the services you offer?  EcoArray has been in business since October 2002.  Since that time, we have run over 60 suppression subtractive hybridizations for 16 different species, constructed 15 libraries in 6 species, submitted 20,000 clones for sequencing, printed seven sets of custom arrays, and developed oligonucleotide arrays for three species.  We have run ten projects with real-time PCR for customers/collaborators located throughout North America and Europe.  
  • Once EcoArray has my samples, how long will it take before I have the results?  Turn-around time depends on the project and how many additional projects are waiting before yours. However, before beginning each project, EcoArray will provide the customer with an estimated time to completion; and we will give you status reports by email as we complete milestones in the project.  For example, this is the optimal amount of time it takes for us to complete a suppression subtractive hybridization library (subtraction):  1-3 days to process and perform quality control on RNA (depending on number of samples); 5 days to run the subtraction, 2 days to ligate into vector and grow clones; 3 weeks in the sequencing lab; 1 week to annotate sequences and get information to customer.  Overall, the customer should expect results in 7- 8 weeks. 
  • After the results are transferred to the consumer, how much help is offered?  EcoArray will provide as much help as is reasonably required after customers receive their products or services.  We will answer questions about protocols, products and services that do not require us to reveal proprietary information.  We can help you with data analysis, generally on a contract basis. 
  • Is there a guaranteed level of quality control for EcoArray products and services (e.g., subtraction libraries, membrane arrays, and glass slide arrays)?  Absolutely.  All of EcoArray’s products (reagents and solutions, nylon membrane arrays) are made to exacting standards, inspected, and guaranteed to work with the recommended protocols.  We also guarantee that all services we provide in our lab will adhere strictly to established protocols and that the results are within acceptable parameters.  Further, we will guarantee that all data has been analyzed correctly.  Agilent will guarantee the quality construction of the probes and spotting of the oligonucleotide array. EcoArray cannot, however, guarantee that you will see significant results for any particular gene or project – that is a function of your experimental design. 

  • Is EcoArray associated with the University of Florida?  EcoArray is a separate “for-profit” company.  Our administrative offices and development laboratory are currently located at the Sid Martin Biotechnology Development Incubator ("BDI") of the University of Florida in Alachua, FL, a facility that encourages the development of biotechnology businesses.  Two of our founders, Dr. Patrick Larkin and Dr. Nancy Denslow, were working at UF when EcoArray began in 2002.  Dr. Larkin now works solely for EcoArray; Dr. Denslow is chairperson of our advisory board and is also a professor at the University of Florida

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2. NYLON MEMBRANE cDNA ARRAYS

  • Must I purchase a minimum number of arrays?  You must purchase a minimum of 4 FHM (200 gene) or LMB (500 gene) membrane arrays.  If EcoArray is printing custom arrays for the species of your choice, you must purchase membrane arrays in multiples of 20. 
  • May I run the arrays in my own lab? You may run the membrane arrays in your own lab, provided you have access to the required reagents and equipment.  Our protocol has been optimized for a-P33 radioactive label.  (You may be able to use a chemiluminescence protocol, but we cannot provide one nor troubleshoot one.)  You will need access to a hybridization oven and bottles, a phosphor image screen, and a scanner to read the screen.  We use a graphical analysis program after scanning to analyze the results. 
  • I do not have a certified radiation lab.  Will EcoArray run these arrays for me?  Yes, EcoArray can do whatever you are not comfortable with in your lab (except exposures).  After you run the exposure experiment and collect tissue samples, EcoArray can process your samples for RNA, check the quality and integrity, DNase-treat, and radioactively label the samples.  We can then hybridize, wash, scan, and analyze the arrays, providing the customer with the raw data and a full report. 
  • What is a typical experiment using membrane arrays?  Typical experiment: Process (label samples, hybridize and wash) 20 arrays containing 200-genes.  Customer provides the DNase-treated, high quality total RNA samples.  Approximate cost: $4,500 academic,   $5,500 commercial
  • Why would I use 200-gene nylon membrane arrays for fathead minnow analysis when the glass slide arrays are available with 2,000 or 22,000 genes?  Cost, ease of use and species.  For customers who would like to run their own arrays, these membranes are an economical alternative, especially if many samples are involved.  They are very nice for novices, as you obtain a manageable amount of data that is easier to analyze than that from the glass slide arrays. Equipment needs are radiation, a hybridization oven and bottles, phosphor imaging screen, and scanner.  If you have questions about what platform may be right for your project, please contact us.
  • How many genes can I put on a custom species membrane array?  The theoretical maximum number of “spots” that can be placed on an array is 1544 (384 x 4).  However, we have found that it is almost impossible to hybridize the arrays with radiation and analyze the spots individually at this density because of overlapping pixel intensity.  We are comfortable spotting a maximum of 772 spots.  This equates to 768 genes plus 4 controls spotted one time each, or 384 genes spotted in duplicate plus 4 control spots.  With more than 768 genes, we recommend an oligonucleotide array, which we can help design for you.
  • If I have only gene sequences, can EcoArray make a custom membrane array?  No.  EcoArray spots cDNA on the nylon membrane arrays.  We must start with glycerol stocks of clones or purified PCR product.  If all you have are sequences, we must determine another way to get you the desired product.   
  • What type of statistical analysis do you offer for the arrays? In EcoArray’s analysis process, we correct for background variation, then normalize the spots both within and between membranes by using several different sets of genes (control spikes, actin, and ribosomal). We calculate mean value (if spotted in duplicate), fold change and p-values for each gene.  The results of each normalization are compared, lending additional support to the arguments for differential expression.  The customer receives a complete report that includes all raw and normalized data, calculations, and tables containing differentially regulated genes. Pricing depends on the size of the project.  We would charge approximately $350 academic, $450 commercial to analyze a project that used 8 arrays with less than 480 genes.

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3. FATHEAD MINNOW OLIGONUCLEOTIDE MICROARRAYS (2,000-gene and 22,000-gene):

  • Must I purchase a minimum number of arrays?  You must purchase a minimum of 6 arrays (3 slides for the 2000-gene array, as there are 2 arrays per slide in the current 11K format; 6 slides for the 22,000-gene array).  In some cases, we may allow you to purchase less (see smallest experiment).
  • EcoArray’s “standard package” for the FHM oligonucletide arrays includes processing by your company.  Can the arrays be purchased individually?  You may purchase the bare array without EcoArray processing, and run the arrays yourself.  EcoArray will assume you have some experience running arrays when you select the “array only” package. 
  • May I run the arrays in my own lab? You may run the arrays in your own lab by purchasing the “array only” package.  Running these arrays requires specialized reagents such as cyanine 3 and 5 dyes, and specific equipment such as a hybridization oven and a scanner that supports the slide format.  However, you will not be able to extract the data in your lab. You must send the image files to EcoArray for feature extraction of the data, which will then be sent back to you. If you are not a member of the Data Sharing Program, we will do NOTHING with your data except return it to you after extraction. You may want to consider the DSP (Data Sharing Program) to take advantage of EcoArray’s special discounts and other benefits.

  • Why must I send the image files to EcoArray for feature/data extraction? EcoArray owns the design files for the arrays and the probes. This information is part of our intellectual property and must be protected from a business standpoint.
  • Will EcoArray guarantee the results from the arrays?  We will guarantee processes, but not results.  First, Agilent will guarantee the quality construction of the probes and array.  If EcoArray processes the arrays in our lab, we will guarantee that the established protocols have been followed and that the processed array images are within acceptable parameters.  Further, we will guarantee that the data has been analyzed correctly.  EcoArray cannot guarantee that you will see significant results from any particular gene – that is a function of your experimental design and the biology of the species.
  • Will EcoArray train me to run the microarrays?  EcoArray does not provide training on how to process the microarrays at this time.  We may consider conducting some training workshops in the future if there is enough interest.  In the meantime, Agilent offers workshops on how to process the oligonucleotide arrays. 
  • Will EcoArray provide technical support to me if I run the arrays in my lab?  Yes.  EcoArray provides protocols and advice on processing on a CD that accompanies all arrays.  We provide additional direct support to DSP (Data Sharing Program) customers.
  • What is a typical experiment? There is no answer for this question as there is no “typical” experiment.  Researchers and industrial users must run as many arrays as required to answer the particular hypothesis and achieve the specified level of statistical significance.  In projects using human arrays, the number of arrays varied from two to several hundred.   Minimum order of this type of array is 6 arrays (3 or 6 glass slides depending on which array you choose).  
  • What is the smallest experiment I can run?  Two arrays.  If all you are looking for is basic data about differential gene expression, it is possible to run two arrays using pooled samples of total RNA.  For an experimental this small,we prefer to run a reference design, combining our reference RNA labeled with Cy-3 with your samples labeled with Cy-5.  One array will be hybridized with your pooled control (plus ref); the other with pooled exposed sample (plus ref).  The data from the two arrays is analyzed to reveal genes that are differentially expressed.   Bear in mind that the sample size for each group is n=1, and this is not likely to give you enough support for publication.  Normally, the minimum order is 6 arrays, but contact us – we may be able to authorize fewer arrays. 
  • What is an ANOVA test? An ANOVA (Analysis of Variance), sometimes called an F test, is closely related to the t test. The major difference is that, where the t test measures the difference between the means of two groups, an ANOVA tests the difference between the means of two or more groups.  A one-way ANOVA, or single factor ANOVA, tests differences between groups that are only classified on one independent variable.  For example, ANOVA is appropriate when testing gene expression between groups such as those that have been exposed to low-dose and high-dose levels of a contaminant, and the controls. 

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4. FHMinnow Data Sharing Program (DSP) and Pricing:

  • What is the EcoArray Data Sharing Program? DSP is a mutually beneficial agreement between EcoArray and the researcher. In exchange for getting the lowest guaranteed pricing on EcoArray FHM oligonucleotide microarrays and reduced cost analysis, the researcher agrees to send the unedited text files to EcoArray. (See the detailed program description.)
  • In exchange for receiving the lowest prices possible (DSP pricing) on the FHMinnow oligonucleotide arrays , what I have agreed to do?
    • You have agreed to run EcoArray’s FHM 2000-gene or 21,000-gene microarrays in an experiment, either with EcoArray doing the processing or with the processing being done in your own lab.
    • You have agreed to use the specified Agilent protocols to run these arrays   (i.e., the Spike-In Kits, one or two color) and use a late model Agilent or Axon scanner to generate the .tif files.
    • You have agreed to purchase 50 microarrays over a period of 2 years
    • You have agreed to provide EcoArray with the image files that are generated after scanning each processed array and EcoArray will feature extract the data to be returned to you..
    • Should you find a biomarker of interest, you agree to notify EcoArray and help us license that biomarker from your institution.. 
    • You agree to a non-competition clause with EcoArray.  Among other things, this means that you will not use any information you gain from the project to produce your own array, offer your processing (labeling, hybridization, scanning, or analysis) services to any other individual or group, or sell (or otherwise provide) the arrays to any other individual or group.
    • You have agreed to publish your results and acknowledge EcoArray in all publications. 
  • What advantages do DSP members receive?
    • Guaranteed lowest pricing on all FHM oligonucleotide arrays containing 2000-genes or more.  This discount is in addition to any discount already given by Agilent (i.e., academic discount). 
    • Members will have access to any and all protocol modifications that will make processing the arrays more economical. 
    • You will be made aware of grant and other collaboration opportunities.
    • When EcoArray has accepted 50 arrays of your data into the FHM database, we will run your data against the entire database at a $3,000 discount from normal bioinformatics prices. 
  • Do I have any restrictions on publishing my data?  Absolutely not.  EcoArray encourages the publication of your data and results.  We will, however, expect to be acknowledged in the publications.
  • What is EcoArray going to do with my data?  EcoArray will place your raw text data and image files on our secure server.  We will never divulge the raw data, although you may choose to do so. You data will become part of our proprietary database, and we run bioinformatics on your arrays and others using the database.   

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5. SUPPRESSION SUBTRACTIVE HYBRIDIZATION (SSH) LIBRARY

  • What is a subtraction library? A subtraction library is a collection of genes that are differentially expressed between two different populations.  Suppression subtractive hybridization (SSH) is one of the most powerful and popular PCR-based methods for isolating differentially expressed transcripts. Using a small quantity of either total RNA or poly A+ mRNA (2.5 ug) from each of two populations, the SSH procedure simultaneously subtracts and partially normalizes the abundance of target cDNAs in the subtracted population.  Two subtraction libraries, forward (“experimental”) and reverse (“control”), are generated by each subtraction protocol. 
  • How many genes do you recommend I sequence? The customer decides how many genes to sequence in all projects.  However, EcoArray requires that genes be sequenced in plates of 96 for maximum efficiency.  For a subtraction library, we recommend two plates of 96 clones (one in each direction).  Depending on the results (i.e., high number of unique genes), it may be advantageous to sequence additional clones from the library, or to sequence from the unsubtracted libraries. 
  • Who owns the clones and information? EcoArray’s policy on ownership is as follows:  The customer owns all products, services, and associated intellectual property in a commercially priced project.  If the customer agreed to an academic/government discount, then EcoArray has the right to use the identified gene sequences, or products used to derive the sequences (i.e., glycerol stocks, PCR products) as part of its commercial product line or to develop commercial products.  This does not restrict the academic/government customer’s right to publish.  If the work associated with the products and services results in publications, EcoArray expects to be acknowledged in the publications. 
  • What are the deliverables? EcoArray will provide the following to each customer upon completion of the subtraction:
    • An Excel listing of all genes sequenced.  All gene sequences belong to the customer.  If an academic discount has been provided, EcoArray reserves the right to use these sequences for commercial use. 
    • Glycerol stocks of the sequenced forward and reverse libraries (96-well plates).
    • If requested, glycerol stocks of the unsubtracted forward and reverse libraries (which may or may not have been sequenced).
    • A two-week trial subscription to Blast Quest.
  • What kit do you use to perform subtractions? EcoArray uses the Clontech PCR-Select cDNA Subtraction Kit (Clontech Kit # 637401). 


  • Will EcoArray train me to perform subtractions in my own lab?  EcoArray is unable to provide training at this time on any services we perform for a fee.

6. cDNA LIBRARY CREATION

  • What is the difference between a normalized and non-normalized library? Both libraries are “snapshots” of the gene expression for a particular organism, tissue and time.  In a non-normalized library, each cell expresses thousands of copies of 10-20 highly abundant genes, hundreds of copies of hundreds (medium abundance) of genes, and only 1-50 copies of thousands of rare genes.  When a cDNA library is normalized before sequencing, the normalization greatly decreases the multiple copies of abundant transcripts. Thus, normalization increases the efficiency of random sequencing dramatically, and is essential for rare gene discovery. 
  • How many genes do you recommend I sequence? The customer decides how many genes to sequence in all projects.  However, EcoArray requires that genes be sequenced in plates of 96 for maximum efficiency.  One plate should be sequenced for each normalized or non-normalized cDNA library.  Depending on the results (i.e., high number of unique genes), it may be advantageous to sequence additional clones from the library. 
  • Who owns the clones and information? You, the customer, own the results of the library.  This includes the glycerol stocks, the sequences, and the BLAST results.  If an academic discount has been provided, EcoArray reserves the right to use these sequences for commercial use. 
  • What does EcoArray provide to me?  Upon completion of the cDNA library, the customer will receive:
    • An Excel listing of all genes sequenced.  All gene sequences belong to the customer. If an academic discount has been provided, EcoArray reserves the right to use these sequences for commercial use. 
    • Glycerol stocks of the library (2.0 ml tubes).
    • A two-week trial subscription to Blast Quest.

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Content

    1. General Questions
    2. Nylon Membrane cDNA
    3. Oligonucleotide Arrays
    4. FHM Data Sharing Program (DSP)
    5. Hybridization Library
    6. cDNA Library Creation
   
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