Stanford: functional genomics facility
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F.A.Q.


  1. Ordering Microarrays:
    1. How do I get set up to order microarrays?
      2.
    2. I'm a non-Stanford-affiliated researcher and I need your Tax ID number before I can order from you. What is that number?
      3.
    3. I'm having trouble logging in to your website. I used to be able to log in with this Username and password! What shall I do?
      4.
    4. The password you sent me is a long, nonsensical number. How can I remember that?
      5.
    5. Your website did not accept the Stanford account number I entered. What is the problem?
      6.
    6. I'm a PI. What safeguards do you have in place to ensure that someone not from my lab can't order microarrays using my account number?
      7.
    7. Can I use a credit card to order from your facility?
      8.
    8. Do you offer quantity discounts?
      9.
    9. Why don't I see an option on your website to order the mouse microarrays?
      10.
    10. I placed an order for microarrays. When will my arrays be ready?
      11.
    11. What is your billing address?
      12.



  2. Microarray Details:

    1. What is a DNA microarray and what can it be used for?
      2.
    2. What type of arrayer do you use?
      3.
    3. On what substrate are the microarrays printed?
      4.
    4. Where can I find information about the clone constitution of the production arrays?
      5.
    5. For the mouse arrays, did the clones come from just one strain or were there multiple sources?
      6.
    6. How are the features(spots) arranged on the SFGF microarray?
      7.
    7. How can I determine whether the clone in which I'm interested is printed on your microarray?
      8.
    8. The clone I'm interested in doesn't seem to be on your arrays. How can I find out if you have this clone stored away in your freezer?
      9.
    9. How can I find out the number of duplicated clones or genes on the array?
      10.
    10. Are there any controls printed on the arrays?
      11.
    11. Is the Doping Control RNA Spiking mixture available to off-campus researchers?
      12.
    12. Can I view images obtained from experiments done using your arrays?
      13.
    13. What is the overlap in gene coverage between the Stanford MM array and the Affymetrix 430 set?
      14.



  3. Working with the microarrays:
    1. How can I get microarray information from the slide barcode?
    2. Do you offer any type of training for new users?
      3.
    3. I am not a Stanford-affiliated researcher. May I still sign up for the hybridization workshop?
      4.
    4. Do you have a scanner that I can use?
      5.
    5. Do you provide a template file for gridding with GenePix?
      6.
    6. I've hybridized,scanned and gridded my microarrays. How can I find out what all those spots are?
      7.
    7. I don't plan to use SMD to store or to analyze my results. Is there any other way that I can obtain information about the spots?
      8.
    8. The spots on my hybridized microarray look strange. What do you think went wrong?
      9.
    9. I've hybridized my arrays and entered the results into SMD. Now I'm trying to find out which clones demonstrate interesting expression results. What is the significance of genes prefixed with ** in the Gene Name column?
      10.
    10. What are the spots with cloneIDs that start with IW or RW(e.g. IW:1)?
      11.
    11. What size coverslip should I use for my hybridization?
      12.
    12. Should I use oligo dT, random hexamers or a mixture for making fluorescently labelled cDNA from my mRNA sample?
      13.



  4. Miscellaneous:
    1. I would like to aknowledge SFGF when I publish the results from my microarray experiments. What is the best way to do this?
      2.
    2. We have DNA ready to print. Will you print it for us?
      3.
    3. My favorite clone isn't on your array. How can I get it added?
      4.
    4. What is an LUID?
      5.



  1.   Ordering Microarrays: 

    1. How do I get set up to order microarrays?
      2.
      Register on our website for a user account. A password will be sent to you immediately! If you work for a PI who is already registered and who has a Stanford account number, find out what the account number is that you should use to pay for the microarrays. You will need to enter this when you place your order. Otherwise, you will need a Purchase Order number to place an order.


    2. I'm a non-Stanford-affiliated researcher and I need your Tax ID number before I can order from you. What is that number?
      3.
      Tax ID: 94-1156365


    3. I'm having trouble logging in to your website. I used to be able to log in with this Username and password! What shall I do?
      4.
      Please use the "Forgot your Password?" link and you will be prompted to enter your email address. You will be sent a new password immediately. If your email address is not recognized, please send a message to       microarray@genome.stanford.edu and we'll fix things for you.


    4. The password you sent me is a long, nonsensical number. How can I remember that?
      5.

      You don't have to remember it! You can change your password by using the "Update Your Profile" section under the sfgf tools menu. You can also update any of the information we have recorded for you such as your address, phone number or your user name.


    5. Your website did not accept the Stanford account number I entered. What is the problem?
      6.

      If you are a Stanford researcher, this means that even though the number is probably a valid Stanford account number, we don't yet have it in the SFGF database.

      As of September 1, 2003, Stanford converted to a new financial software system and each account number must be converted to a new format. SFGF has converted all the account numbers that we had stored for you. If you need help converting an old number to the new format, go the ordering page as if you plan to place an order and use the link to the Stanford converter.

      If you are a PI, you can add account numbers to our database by logging in to microarray.org and then going to the "Update Your Profile" section. You can also mark an account number as inactive and then nobody will be able to order using that number. Then you must select an approver for the account number from the approver menu. If your approver is not on the menu, send an email containing the account number and the approver's name to       microarray@genome.stanford.edu.

      If you are not a PI but you want us to add an account number to our database, you can send the information to microarray@genome.stanford.edu..

      If you do not have a Stanford account number, you can use a PO number.


    6. I'm a PI. What safeguards do you have in place to ensure that someone not from my lab can't order microarrays using my account number?
      7.

      When a user registers for an SFGF account, an email is sent to the PI whom the user has listed. You can notify us if someone who is not one of your lab members has registered under your name. In addition, whenever a microarray order is placed by a person whom we have listed as part of your lab, the only account numbers accepted are those that are listed under your name. If a person not registered as part of your lab knows one of your account numbers and attempts to order using this number, the order will not go through. Finally, each time an order is placed, a message is sent to the approver listed for the account number which is entered. This approver must log in to the SFGF website and click approval before we can make an invoice for the order.


    7. Can I use a credit card to order from your facility?
      8.

      No.


    8. Do you offer quantity discounts?
      9.

      No. Because we are a government service center, we operate under very strict accounting and pricing rules, and we cannot be that flexible.


    9. Why don't I see an option on your website to order the mouse microarrays?
      10.

      It is probably because your PI is not listed in our database as a Stanford-affiliated researcher. Currently we are allowed to distribute the Mouse arrays only to Stanford researchers. If your PI has a Stanford account number, we can sell the Mouse arrays to you.


    10. I placed an order for microarrays. When will my arrays be ready?
      11.

      You can check your position in the ordering queue from the website by clicking on "Ordering Queue" in the SFGF Tools menu. If you need an estimate on time of delivery and/or to know which type of array we are currently printing, please contact the Production Manager, Elena Seraia, or send email to       microarray@genome.stanford.edu.


    11. What is your billing address?
      12.
      Stanford Functional Genomics Facility
      Attn: Luisa Jimenez , MC 5177
      CCSR, 269 W.Campus drive
      Stanford, CA 94305-5176







  2.   Microarray Details: 

    1. What is a DNA microarray and what can it be used for?
      2.

      Please refer to the NCBI primer on Microarrays at http://www.ncbi.nlm.nih.gov/About/primer/microarrays.html


    2. What type of arrayer do you use?
      3.

      We use the Stanford-UCSF style microarray printer.


    3. On what substrate are the microarrays printed?
      4.

      They are printed on glass microscope slides which are coated in-house with Poly-L-Lysine or on Corning GAPSII or UltraGAPS slides.


    4. Where can I find information about the clone constitution of the production arrays?
      5.

      From the main menu, select "Services" and then "Production array".


    5. For the mouse arrays, did the clones come from just one strain or were there multiple sources?
      6.

      Multiple strains were used. To check the sources of the mouse libraries, select "Services" and then "Production array" from the main SFGF menu. Strains listed by our main sources of mouse clones include C57Bl/6, SV129, FVB and B5/EGFP transgenic ICR mice.


    6. How are the features(spots) arranged on the SFGF microarray?
      7.

      The current MM array edition contains 48 sectors of 30 rows and 30 columns of spots in each sector, printed at 146 micron spacing. The recent SH arrays have been printed with 30 columns per sector and with 29 or 30 rows in each of the 48 sectors. The spot diameter is 80 - 90 microns. For details about your particular array batch, please refer to the QC notes page of the website(you must have an SFGF account and be logged in to access the QC notes page).

      The total possible number of spots that we can fit into this configuration is 43,200, and there is one array per slide.

      If one orients the array with the barcode at the bottom, the sectors are numbered with #1 in the upper left-hand corner, 2-4 proceeding to the right, 5-8 in the second row of sectors, and so on.

    7. How can I determine whether the clone in which I'm interested is printed on your microarray?
      8.

      From the SFGF home page, select "Gene Search" from the "sfgf: tools" menu.
      Using this program, you can search a particular array batch for clones of interest. If you don't know which batch to search because you do not yet have your microarrays, select the print log from the most recent print run. For Mouse, the batches are labeled with prefix MM followed by a batch designation in alphabetical order(i.e. the sequence is MMA, MMB, MMC ?).
      For Human arrays, the SH prefix is followed by A-Z, then AA-AZ, BA-BZ, CA-CZ, DA - DZ, EA -> and so on.


    8. The clone I'm interested in doesn't seem to be on your arrays. How can I find out if you have this clone stored away in your freezer?
      9.

      Use our "Clone Library" search under SFGF tools. With this, you can search our entire library of clones!


    9. How can I find out the number of duplicated clones or genes on the array?
      10.

      From the SFGF home page, select "Gene Counting" from the "sfgf: tools" menu. See the previous answer for help in selecting which print log to search.


    10. Are there any controls printed on the arrays?
      11.

      On some Human array batches, we have included a set of "Doping" or "Spiking" controls, named as such because we have an RNA mixture corresponding to the DNAs in these control spots. The printed controls include many copies per array of GAPD along with various sized PCR fragments from Methanococcus jannaschii. You can obtain the RNA mixture from us to include in your labeling reaction.


    11. Is the Doping Control RNA Spiking mixture available to off-campus researchers?
      12.

      We are not equipped to ship the RNA, so it is available only to researchers who can pick it up in person.


    12. Can I view images obtained from experiments done using your arrays?
      13.

      Yes! Log in and then go to our "Array QC Notes" page (from the SFGF tools menu) and take a look!


    13. What is the overlap in gene coverage between the Stanford MM array and the Affymetrix 430 set?
      14.

      The current edition of the MM array(e.g. MMZ) shares at least 14,776 Unigene Cluster IDs with Affymetrix 430A plus 430B. We don't have the cluster ID information for all clones, so the overlap is probably larger. This comparison was based on annotation from Unigene Build 124(released 8-12-2003) for the MM array and annotation from 6-15-2003 for the Affymetrix array.


  3.   Working with the microarrays: 

    1. How can I get microarray information from the slide barcode?


      1. Log into your SFGF account.
      2. Click on "sfgf:tools" -> "Array Info".
      3. In the textbox, enter the barcode number that is printed on your microarray and click on the submit button.
    2. Do you offer any type of training for new users?
      3.

      Yes! We offer a hybridization, scanning and gridding workshop, for which you can register online AFTER you have received your microarrays (See "Hybridization Class" in the "Services" menu). The Stanford Microarray Database (SMD) at       http://genome-www5.Stanford.EDU/MicroArray/SMD/ periodically offers an Introductory Tutorial; this covers details of loading your experiments into SMD and the basics of working with the database. This tutorial is available on video from the SMD Help pages.


    3. I am not a Stanford-affiliated researcher. May I still sign up for the hybridization workshop?
      4.

      No, we're sorry but for now we don't have time to train external users.


    4. Do you have a scanner that I can use?
      5.

      Yes, we have Axon and Agilent scanners for which you can sign up online. See the ordering page for current pricing. The Agilent scanner is the G2565AA Microarray Scanner System, which can hold 48 slides at once!


    5. Do you provide a template file for gridding with GenePix?
      6.

      Yes! Go to our "Array QC Notes" page and click on the .gps file for your batch to download a template gridding file(you must be logged on to access this page).


    6. I've hybridized , scanned and gridded my microarrays. How can I find out what all those spots are?
      7.

      One way to do this is to enter your hybridization results into the Stanford Microarray Database (SMD at       http://genome-www5.Stanford.EDU/MicroArray/SMD/).

      You will need to apply for an account, which you can do either by filling out the SMD registration form linked from the URL above or by selecting the option to also apply for an SMD account when you register for your account with SFGF. Once you have your SMD account, you can enter your data from GenePix(Axon) or ScanAlyze into SMD and it will become associated with annotation for the spots.

      Beginning in 2004, there will be a usage-based charge for loading experimental data into SMD.


    7. I don't plan to use SMD to store or to analyze my results. Is there any other way that I can obtain information about the spots?
      8.

      Another way you can obtain information about spot annotation is to download the .gal file for a print run directly from our website. To do this, log in to microarray.org, select "Array Info" from the sfgf:tools menu and then enter the label or barcode of your microarray. You will be able to access various information, including a .gal file for the print run.

      You can also download a .gal file from SMD by following the "Print List" link from the "List Data" Menu and then clicking on the ".gal file" icon corresponding to the name of the print which corresponds to your slides. This .gal file is a list of Block/Column/Row positions and the cloneids of the spots. To be able to do this, you will need to register for an SMD account.


    8. The spots on my hybridized microarray look strange. What do you think went wrong?


      9. Corning has made available a microarraying trouble-shooting guide at       http://www.corning.com/lifesciences/technical_information/techdocs/troubleshootingUltraGAPS_ProntoReagents.asp#a5
      There are some very helpful images that demonstrate the results of various problems that can occur in the hybridization process.


    9. I've hybridized my arrays and entered the results into SMD. Now I'm trying to find out which clones demonstrate interesting expression results. What is the significance of genes prefixed with ** in the Gene Name column?
      10.

      The double asterisk indicates that in Unigene, the clone is listed as mapping to two different clusters. The clone might overlap two genes, or the accession numbers for the 3' and for the 5' ends may have been assigned to different clusters by Unigene.


    10. What are the spots with cloneIDs that start with IW or RW(e.g. IW:1)?
      11.

      These are clones from Stanford investigators and we don't know any more about their identity yet. Both sets of clones have been sequenced recently and as soon as the investigators identify the genes to which the sequences correspond and let us know, we will update the information in SFGF and SMD.


    11. What size coverslip should I use for my hybridization?


      12. For the 48 sector arrays, we use 22 x 60 mm coverslips or 24 x 60 mm lifterslips.


    12. Should I use oligo dT, random hexamers or a mixture for making fluorescently labelled cDNA from my mRNA sample?


      13. We don't recommend using random hexamers or mixing them in when making labelled cDNA from poly A+ RNA unless you are confident of the purity of the mRNA. If you have contaminating rRNA or genomic DNA, you will want to avoid making labelled DNA from these. It is safer to use anchored oligo-dT primers.

  4.   Miscellaneous: 

    1. I would like to aknowledge SFGF when I publish the results from my microarray experiments. What is the best way to do this?
      2.

      We appreciate it if papers acknowledge us in the following way (or something similar):
      "We would like to thank Michael Fero and the staff of the Stanford Functional Genomics Facility for supplying us with the human cDNA microarrays used for this study."
      You might also mention in a footnote that:
      "Large scale human cDNA microarrays similar to the ones used for this study are available to researchers at not for profit research institutions by contacting the Stanford Functional Genomics Facility, CCSR 4256, 269 Campus Drive, Stanford, CA 94305-5177 or by visiting www.microarray.org."


    2. We have DNA ready to print. Will you print it for us?
      3.

      Yes, if it is from another species besides Mus musculus and Homo sapiens.
      Please refer to the ordering page for pricing, and then contact us at       microarray@genome.stanford.edu to work out the details.


    3. My favorite clone isn't on your array. How can I get it added?


      4. We are happy to add clones to our array under the following conditions:
      EITHER: Clones are in plasmid format and we are able to use our primers (AEK for human array and pSPORT or T3/T7 for the mouse array) to amplify. AEK is very similar to M13 so M13 is acceptable. The primer sequences we use are:

      AEK-F: 5'-TTG TAA AAC GAC GGC CAG TG-3'
      AEK-R: 5'-CAC ACA GGA AAC AGC TAT G-3'

      pSPORT-A: 5'-CCA GTC ACG ACG TTG TAA AAC GAC-3'
      pSPORT-B: 5'-GTG TGG AAT TGT GAG CGG ATA ACA A-3'

      T3: 5'-AAT TAA CCC TCA CTA AAG GG-3'
      T7: 5'-AAT ACG ACT CAC TAT AGG G-3'

      OR: You supply the clones after PCR and precipitation, ready to be rehydrated in 3X SSC and printed.


    4. What is an LUID ?


      5. LUID stands for Laboratory Unique Identifier. It identifies the plate-well-column location from which a DNA originated. You can find this information in the SMD raw data file for your experiment.


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