FAQ
Project Planning Questions
Q: I cannot fill a 96-well plate as I do not have enough samples. Do you allow partial plates?
A: No, we do not accept partial plates. Please duplicate samples that may be biologically interesting to you to fill the plate. e.g. multiple copies of parental DNAs or valuable/ irreplaceable specimens
Q: Do you have a sole source statement?
A: No. There are companies that offer GBS services under a different name (e.g. RAD or SGB) so we are not the only facility that performs next-generation genotyping.
Q: What is the turnaround time for GBS?
A: Turnaround time for library preparation and DNA sequencing is usually 2 months from receipt of samples. If data analysis is requested, turnaround will be a few weeks longer. Please let us know in advance if you have a project deadline.
Preparing a Submission
Q: How do I submit my plate information for review?
A: Once your project has been approved and PO number/service contract has been uploaded, click the "Create Plate" button at the bottom of your project page. You will then be able to download a template for recording sample information. Once the required template fields are completed, upload the sample information and gel images. Click “submit” once you have made all edits to the template so your plate may be reviewed. You will need to submit a separate template for each plate.
Q: My samples are ready! May I ship them?
A: No, you may only ship samples once your plate(s) or optimization sample(s) have been approved for shipping. Project approval is not the same as sample approval.
Samples sent without approval cannot be barcoded for tracking security within the lab and may cause project delays, incur additional storage fees, or be returned at the User’s expense.
DNA Extraction
Q: Do you have an extraction kit recommendation?
A: We use Qiagen DNeasy Plant DNA isolation kits. This column-based kit can be purchased in single tube or 96-well formats. For animal DNA extractions we recommend Qiagen blood and tissue kits.
Uploading Files and Templates
Q: I get an "incorrect number of columns" error message when trying to upload my plate’s completed template. How do I fix this?
A: After downloading the template, open the text document in Excel. You may need to tell the program to look for all files. Depending on your version of Excel and settings, the document will open and (A) it will launch the "convert text to columns wizard" or (B) show all data in column A.
(A) follow the wizard : step 1 - select delimited, step 2- select Tab, step 3- default for "column data format" should be general, select finish.
(B) Select column A (the entire column should be highlighted), go to the data tab, and select "Text to columns" then follow the wizard using the instructions listed above in (A).
After you have made edits save the file again as a tab delimited and try uploading again.
Q: What information is required in the template for the blank (empty) well?
A: You do not need to include any additional information. This row should only contain the text “BLANK” under the sample name column, as it appears in the empty template you originally downloaded.
Q: After uploading my template file I received a warning about low concentrations. What does this mean?
A: This message is a summary of the concentrations reported in the uploaded template file and does not necessarily mean that your samples will not be approved. When your plate is reviewed, if 10% or more of listed concentrations are equal to or less than 10 ng/µL, you will be notified that concentration may not be appropriate for GBS.
Q: After uploading my template file I received a warning about high concentrations, does this mean I need to dilute my samples?
A: Yes, please dilute high concentration samples to fall within the range of 30 -100 ng/ µL. Failure to do so may result in your project incurring additional processing fees and delays.
Q: I am trying to upload an updated template with altered sample locations but all the upload buttons are gone from the plate’s page. How do I submit this?
A: If a plate has already been approved or rejected by a reviewer, you will no longer be able to alter the sample information of the plate. If you need to change the location of samples on an approved plate, you will need to create a new plate within your project to submit information to us. Please notify an admin via conversations, to reject the original plate.
Q: Can I rearrange the order of the species in the plate?
A: No, you cannot alter the order of species on the plate. Samples should be arrayed to match the template generated by our LIMS.
Sample Test Digests and DNA Quality
Q: Can I use a ladder other than the Lambda HindIII mass standard?
A: Yes. If you use a different type of marker, label the image clearly with the type of ladder used.
Q: What samples should I include in the 10% test digest?
A: The samples included in your test digest should be a random sampling of the individuals you plan to submit for GBS. If you would like to sample without replacement, including parents of a population, individuals from different extracts, collection times, and populations as part of your test is advisable. If you are submitting multiple species, all should be represented in the test digest. See our User Guide section “DNA quality control” for full instructions.
Shipping Samples
Q: Do you have a preferred courier service?
A: We have no preference. You may use any courier you prefer.
Q: Do you receive packages on weekends or holidays?
A: No, we are not able to receive packages on weekends and University Holidays. Please see Cornell's calendar of holidays (https://hr.cornell.edu/policies/all/staff_holidays.html) if you are not sure when we are open.
Q: How should I seal my plates for shipment?
A: Heat seals or well-fitting caps are the only allowable methods. All other forms of sealing will result in the rejection of your plate. Please see our User guide section “Sample shipment” for full instructions.
Q: Should I ship the samples on dry ice?
A: It is not required that you ship samples on dry ice. Please see our User guide section “Sample shipment” for full instructions.
SNP Calling Services
Q: What information is included with the SNP calling service?
A: In addition to your raw sequencing results (fastq files) and basic QC data, we will call SNPs using the TASSEL 3.0 GBS pipeline using the reference genome of your choice for alignment. You will be provided with 1) SNP calls in VCF format, 2) GBS tag sequences and alignment coordinates in SAM format, and 3) a comprehensive data report that includes information for replicating the analysis. For species without a reference genome, the non-reference UNEAK pipeline is available, but not recommended in all situations. Please inquire.
Billing Questions
Q: How do I arrange prepayment?
A: Because of auditing protocols enforced by Cornell Administration, we cannot accept prepayment for work. The earliest that we can invoice is after approved samples have arrived and passed our quantification QC.
Q: May I split my project into multiple invoices?
A: We cannot split credit card charges. However, we can bill different line items to different people/institutions, if requested, as long as all billing contacts are registered with slims.biotech.cornell.edu. Please let us know in advance if you will be requesting multiple invoices.
Version 2 Updated 2016-02-12