Policies

GTAC Policies


Experimental design:
Please contact us if you have any questions about designing your experiment. We provide consultation at no cost. Potentially, a simple consult could save thousands of dollars from a failed experiment.
 
Sample queue:
All samples are processed as they are received. We do not give priority to any sample based on investigator or institution. If there is a QC problem with one of your samples, we will contact you and wait for your decision to move forward, replace samples, or cancel. Once you have approved the QC, the sample/submission will be entered into the queue. Samples that are being repeated due to GTAC error will be placed at the top of the queue.
 
Billing:
We generate invoices on a monthly basis. We cannot bill for a project until the process has been completed. For Washington University investigators, we require the department billing number upon submission. For non-Washington University investigators, we require a hard copy of the PO with the submission to begin processing. Please note that multiple invoices may be sent for a single project.  (For example, if library preparation and sequencing are requested for a single project, two invoices would be sent as these services will be completed at different times.)
 
It is often requested that an invoice be sent immediately upon export of the data, so that money can be used from a grant that is expiring.  In most cases, grants will continue to pay out after the date of expiration, as long as the service was completed within the grant timeline.  GTAC lists the date of service on the invoices, so expedited invoicing is usually not required.
 
Publications:
If data generated by GTAC is used in an abstract, publication, or other formal communication, could the submitter please include the following acknowledgement:
 
“We thank the Genome Technology Access Center in the Department of Genetics at Washington University School of Medicine for help with genomic analysis. The Center is partially supported by NCI Cancer Center Support Grant #P30 CA91842 to the Siteman Cancer Center and by ICTS/CTSA Grant# UL1 TR000448 from the National Center for Research Resources (NCRR), a component of the National Institutes of Health (NIH), and NIH Roadmap for Medical Research. This publication is solely the responsibility of the authors and does not necessarily represent the official view of NCRR or NIH.”
 
Sample retention:
GTAC will maintain excess samples for at least 90 days after completion of the study.  If you would like to have that material returned, please contact us after you receive your data to set up a time to pick it up.
 
Completed sequencing libraries/amplified materials (any remaining products from any of the services that we provide) will also be stored for at least 90 days after completion of the service.  These materials can also be picked up upon request.
 
Sequencing submissions:
We accept sequencing libraries generated in your own lab, or we can handle the entire process of library prep and sequencing for you. We can assist with QC of your starting material if you are planning to prepare your own sequencing libraries. 
 
We require all samples be submitted with the correct submission form. Samples received without submission forms, or forms missing required information will not be processed until complete information is provided.
 
We ask that samples be provided in 1.5ml tubes, with the label matching the sample name on the submission form. For direct to sequencing submissions, please include the lab name and date on the tube. If submitting more than 30 samples at a time, please submit them in a 96 well plate labeled with the lab name and date.
 
Quality control for next-generation sequencing:
All samples received will be quality controlled based on submitted material type:
Genomic DNA– concentration assessed by Qubit, integrity assessed by bioanalyzer/Tapestation
Total RNA– concentration assessed by Qubit, integrity assessed by bioanalyzer/Tapestation
ChIP DNA– concentration assessed by Qubit, size range assessed by bioanalyzer/Tapestation
Pooled Amplicons– concentration assessed by Qubit, size range assessed by bioanalyzer/Tapestation
 
We will contact you if your samples do not meet our input requirements.  You may decide to cancel the prep at this time and only be charged for the QC performed.  Otherwise, you may choose to proceed with the prep, but you will be charged for the prep regardless of its success.
 
All libraries we prepare will be assessed for concentration and size. If we feel the library will not perform well when sequenced, we will send the library QC data to you to allow you to choose whether or not to go forward with sequencing.
 
Libraries that are submitted directly to sequencing will have concentration assessed by Qubit and size range assessed by Agilent Bioanalyzer. We will use these values to calculate your molar concentration unless otherwise specified. If there is large presence of dimers, unusual size distribution, or if there is too little volume to achieve the specified loading concentration, we will contact you to choose how to proceed.
 
Next-generation sequencing specs:
For our standard runs, we offer sequencing per lane.  We do not offer to split lanes between projects or investigators. If you do not require a full HiSeq lanes worth of reads, we also offer MiSeq sequencing runs that obtain ~1/10th the reads of a HiSeq 2500 lane. Standard HiSeq 2500 runs are 1x50+7bp index read or 2x101+7bp index read. For HiSeq3000 runs we offer 1x50+7bp index, 2x75+7bp index, 2x150+7bp index. For MiSeq runs, we offer 2x150 or 2x250 with index reads. We may be able to accommodate different index read lengths if requested at time of submission, you must let us know if your samples require dual index reads.
 
Adhering to Illumina-defined standards, if we obtain suboptimal read numbers or data quality due to an error on our part, we will rerun the lane at no additional charge to the consumer. We do not guarantee sequencing quality or read numbers for libraries that we did not prepare, non-standard library preps, or samples failing any of our QC metrics. This includes samples that are submitted to us for final QC quantitation and pooling, we cannot guarantee overall read number or individual sample reads. For sequencing runs that encounter an instrument error, we will contact Illumina’s technical support.  If they determine that the run or lane was a failure because of a machine or a reagent problem on the sequencer, the sample will be rerun at no cost to you.
 
We include a control PhiX library spiked at 1% into every lane. For direct to sequencing submissions, if a library fails to generate clusters, but the PhiX library is observed, you will be charged for that lane.  If no clusters are observed, we will contact Illumina’s technical support to identify the run failure. If you request that PhiX not be used, you will be charged for the lane regardless of performance. For samples with poor base diversity, we recommend that you request a higher phiX percentage to account for that, we cannot guarantee read numbers for imbalanced libraries. Any HiSeq 2500 samples that are not run as 1x50 or 2x101 will be considered custom runs, and we require you to fill the both lanes of the rapid run flowcell. HiSeq 3000 runs require 8 lanes to run any non-standard read lengths.
 
We can accommodate samples using custom priming, however, these lanes are considered custom and will be charged to you regardless of performance. If you require custom primers, we strongly suggest that you run two lanes on a custom HiSeq 2500 rapid run to ensure that your custom primer will not interact with the other samples on the flowcell. If there is an issue with other lanes of a custom primed flowcell, you will be responsible for the charges of the entire flowcell.

For direct to sequencing samples, we ask for the desired loading concentration. If you do not provide one we will attempt to load the sample at a reasonable concentration based on the size range and type of sample provided for the requested run type. We cannot guarantee optimal density particularly if the sample has an unusual size range. Subsequent submissions can be shifted up or down to better optimize density if you let us know the prior sample for comparison. We do not recommend mixing samples of different prep types onto the same lane as there is a size bias that could cause uneven representation of samples that is beyond our control.
 
Sequencing analysis:
We offer “tier 1” analysis on all sequencing runs. Please view the analysis page to see what is offered for different experimental types. This analysis is provided at no additional charge for a subset of species when requested at the time of sequencing.  If analysis is not requested at the time of sequencing, or additional analysis is requested at a later date, our hourly rate will be applied. If an annotated genome exists for a species that we do not support, we may be able to configure it into our analysis pipeline for a nominal fee.  Analysis beyond what is listed on our website may be available based on scope of the analysis and available resources.  Custom analyses will be subject to the hourly rate and approval from the bioinformatics team.
 
We will supply you with links to access your data that are active for 30 days. We will store the raw and analyzed data for six months from the date it is sent to you. We suggest that you download and store your data. Due to storage limitations, we will be unable to retrieve data older than six months. If you want us to download the data to a hard drive, you must supply the drive with your submitted samples as well as shipping instructions and your FedEx account number. Data downloads or hard drive requests after the initial 30 day period will be charged at the standard bioinformatics rate.
 
Microarray submissions:
We can accept prepared/labeled material - ready for microarray hybridization - that is generated in your own lab.  More commonly we accept RNA or DNA and perform the entire process of preparation/labeling for you. We can assist with QC of your starting material if you are planning to prepare your own labeled material.
 
We require all samples be submitted with the correct submission form. Samples received without submission forms, or forms missing required information will not be processed until complete information is provided.
 
We ask that samples be provided in 1.5ml tubes, with the unique label matching the sample name on the submission form.  As well, please include concentration, PI and date.
 
Quality control for microarray:
Prior to target synthesis, GTAC microarray will evaluate all submitted RNA and DNA for integrity, purity and concentration. Investigators will be notified by email of all specimens that do not meet Quality Control criteria.
 
If processing is canceled upon review, investigators will only be charged for the QC performed. Samples that do not meet our initial QC specifications will require an email confirmation if you wish to proceed with processing. You will be charged for the full service regardless of the outcome.
 
cDNA/aRNA bioanalyzer and nanodrop profiles are checked after amplification to confirm banding pattern and ample mass production. If profiles or mass output does not meet our specifications, you will be emailed the results of the failure. If a repeat processing is requested and failure is incurred a second time, you will be billed for this second failure, as well. If processing is repeated upon request and is successful, you will not be billed twice.
 
Microarray exports and analysis:
Affymetrix:
Microarray data are available for download via a dropbox link. A spreadsheet containing formatted intensity data in log2 scale and with added annotation will be included. The link will be kept active for only 10 days. Please be certain to store your data in a recoverable location.
The raw chip data .CEL along with .ARR can be loaded into Affymetrix Expression Console (freely downloadable at www.affymetrix.com) to export intensity data, or you can load the raw data into Partek Genomics Suite for advanced analysis (license can be obtained through the Becker Medical Library at the University).
 
Alternatively, the spreadsheet format of intensity data can be loaded into a number of other software including the University licensed Spotfire for your data analysis. Please contact help@bmi.wustl.edu to obtain instructions and the product keys to download and install this software (Spotfire).
 
Illumina:
Raw microarray data are available via URL(s). The data will be available from these locations for 10 days. The data is provided in tab-delimited format and normalized by Illumina's average, cubic spline, and quantile methods. Non-normalized background-subtracted and non-normalized raw data will be provided. Data is also provided in “Partek-ready” format.  Please note that these data, when opened in Partek software, are shifted to contain all positive numbers based on the lowest negative number in the average-signal dataset.  Average-signal values are then log2 transformed. Each row represents a gene.  The four columns per sample run thusly:
•AVG_Signal - Average intensity of the Bead Type/target in the group.
•Detection p-value - A non-parametric comparison of the gene value with the ~1000 different ranked negative controls.  A gene with a p-value <0.01 is brighter than 99% of the negative controls.
•Avg_NBEADS - Average number of beads per bead type representing probes for the gene.
•BEAD_STERR - Average standard error associated with bead-to-bead variability for the samples in the group.
 
Agilent:
Agilent raw microarray data is available via URL(s). The data will be available from these locations for 10 days.  Raw data from each microarray hybridization can be found in the individual .txt files.  Please see the ‘experiment information’ Excel file, which dictates the location of the sample(s) on each array (.txt file).  The .txt data files contain the necessary gene signal intensities for downstream analysis.  The .txt data is the full export from Agilent Feature Extraction software.
 
Advanced Analysis:
The Genome Technology Access Center (GTAC) offers fee-for-service advanced analysis of your microarray data. We provide a free initial consultation to discuss your project and offer several tiers of analysis packages to best suit your needs. Please contact gtac@genetics.wustl.edu for additional information.