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Northwestern University Feinberg School of Medicine
Center for Genetic Medicine
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DNA/RNA Quality Control

DNA Quality Control

 

On-chip electrophoresis of DNA samples allows for rapid, direct analysis of a variety of DNA products without the hassle of pouring, running and photographing agarose or polyacrylamide gels. DNA LabChips® contain an interconnected set of fluidic microchannels, which are primed with a fluorescent gel-dye matrix. DNA fragments are separated electrophoretically based on their size as they migrate through the matrix and visualized through fluorescent emission. Data are recorded as a fluorescent electropherogram, which is also presented as a gel-like image for easy comparison to traditional separation methods.

For more information, please visit the Agilent website.

DNA Quality Control Pricing

DNA quality control costs are listed on the Core Pricing page.

Questions

 Types of Chips

There are four analytic ranges available. Three of the ranges, 25-1000bp, 100-7500bp and 100-12000bp, require a starting concentration of 0.5-50ng/uL of DNA. Nanodrop quantitation and dilution services are available at a nominal additional cost to bring samples of unknown concentration into this range. Only 1uL of sample is required for the assay, though we generally ask for at least 4uL, required in cases where concentration needs to be determined, and so that Core staff can troubleshoot and repeat assays if needed.

There are slight variations between the accuracies of fragment sizing and quantitation both within and between the different ranges. Feel free to contact the NUSeq Core staff to discuss selection of the appropriate range for your samples. The fourth analytic range is for High Sensitivity DNA, designed for analysis of DNA in the picomolar range, down to a starting concentration of 100pg/uL, and covering a range of 50-7000bp. This assay is designed for analysis of low-concentration DNA samples for next-gen sequencing, ChIP assays or sheared DNA, with fragment quantitation as low as 5pg/uL.

 Sample Preparation

Each chip can accommodate up to 11 DNA samples (10 samples for High Sensitivity), plus an internal control (supplied by the Core). Only a single range can be analyzed on an individual chip. Please submit samples in 0.5ml or 1.5ml tubes, NOT PCR tubes. For all samples, please indicate your elution or re-suspension media if other than water. High salt concentrations can inhibit mobility through the microfluidic channels, so resuspension in water is recommended.

 Order Submissions

All orders are handled through the NUcore submission system. Core technicians will gladly show you how to submit orders in NUcore if you are unfamiliar with the system. Please follow the directions below to submit samples through NUcore:

1. Go to https://nucore.northwestern.edu/facilities
2. Click on "Login" at the top right-hand side of the page
3. Enter your NetID and password
4. Click on "NUSeq"
5. Click on the link for the service you want (Example: Bioanalyzer - Quality Control Nanochip)
6. Click "Add to Cart"
7. Select the payment source (chartstring number) and click "Continue"
8. Enter the quantity and click "Update"
9. Fill out and upload the completed order form
10. If your order is complete, click on "Purchase", otherwise click on the "Home" tab on the top left-hand side of the page and repeat Steps 4 through 10

 Sample Submission

There are several ways you may send your samples to the core:

If you are located on the Northwestern University Chicago campus:

Bring your samples directly to the facility:

300 E. Superior St.
Tarry 2-770
Chicago, IL 60611

If you are on Northwestern University's Evanston campus:

Drop off your samples at the Molecular Biosciences Administration office (office location below) to be mailed to our facility. Please label the envelope with your name and the number of reactions.

Department of Molecular Biosciences Administrative Office
Hogan 2100
2205 Tech Dr.
Evanston, IL 60208

The couriers pick up the samples every morning and we receive them in the afternoon.

If you are not located on Northwestern University's campus:

Please send your samples through an independent carrier such as FedEdx or UPS.

Our mailing address:

NUSeq Core
300 E. Superior St.
Tarry 2-770
Chicago, IL 60611

Prior to shipping, please contact a technician to schedule delivery. At the time of shipping, please send an email notification with your express mail tracking number. This will allow us to watch for your shipment. We prefer that samples are sent overnight on Monday or Tuesday so that we can guarantee someone is here to accept them. We will notify you when your shipment is received.

 Turnaround Time

Results are generally delivered within one to two business days.

 Results

Results will be delivered as a PDF file, including an electropherogram, gel-like image, and a table indicating the identified peaks and their approximate sizes and concentrations.

All electronic data produced by the NUSeq Core Facility is stored on servers for one year from the date it is made available to customers. Electronic data includes sample, project, and results data files, such as .xsq, .xad, .xls, .txt, .tif, or .jpg files. After the one year retention period, the data will be deleted from the servers. If you have questions about our data retention policy or need to request an additional copy of your data within the one year retention period, please contact nuseq@northwestern.edu.

 Sample Disposal

The NUSeq Core retains submitted samples for two weeks following the completion of a project. If you would like the remainder of any sample to be returned at the completion of the project, please notify the core technicians when you submit your samples and they will be marked for return. Please collect the samples from the core within two weeks of receiving your results. After that time, the samples will be disposed of. The core will not send reminders prior to disposing of the samples.

RNA Quality Control

 

RNA quality analysis via gel electrophoresis requires large inputs and quantification is imprecise at best. The core facility uses the 2100 Bioanalyzer from Agilent to evaluate the quality of RNA samples on three different scales, using only small amounts of RNA. The microfluidics platform electrophoretically separates RNA based on size, giving an electropherogram readout that is also translated into a gel-like image. For total RNA quality analysis, comparison with samples in Agilent's RIN Database allows for algorithmic calculation of an RNA Integrity Number (RIN), a fast and easy indicator of overall RNA quality. High quality RNA samples are needed for many downstream applications, such as microarray analysis. For specific analysis of small RNAs, including miRNAs, the Small RNA assay provides separation of nucleic acids below 150nt. Assay results are usually available within two working days. The facility runs the samples and charges per chip. See below for information about sample number and concentration to determine the appropriate analysis for your samples.

For more information, please visit the Agilent website.

RNA Quality Control Pricing

RNA quality control costs are listed on the Core Pricing page.

Questions

 Types of Chips

Nano chips can accommodate up to 11 user samples. Though the chip accommodates 12 samples total, the Core facility prefers to include an internal positive control of known RIN with each chip. The concentration of samples using the Nano chip must be 50ng/uL - 500ng/uL. A dilution will be made and charged to your account for any samples greater than 500ng/uL. Volume should be at least 4uL. Concentrations below 50ng/uL can be diluted down to Pico chip range.

Pico chips can accommodate up to 10 user samples. Though the chip accommodates 11 samples total, the Core facility prefers to include an internal positive control of known RIN with each chip. The concentration of samples using the Pico chip must be between 0.5ng/uL 5ng/uL. A dilution will be made and charged to your account for any samples greater than 5ng/uL. Volume should be at least 4 microliter.

Small RNA chips can accommodate up to 11 user samples. At this time, the Core does not have an internal positive control for this assay. For total RNA preps, the concentration of samples must be between 10ng/uL - 100ng/uL. For RNA preps that have been enriched for small RNAs (<150nt), the upper concentration limit is 20ng/uL. The quantitative range of the assay is 50-2000pg/uL of miRNA, so the overall concentration should be inversely proportional to the degree of enrichment. For highly enriched samples, we recommend submitting multiple dilutions to ensure the quantitative range is not exceeded. Volume of each sample should be at least 4 microliter.

If you have any questions about assay selection or sample preparation, please contact us

 Sample Preparation

Please submit samples in 0.5ml or 1.5ml tubes, NOT PCR tubes. For all samples, please resuspend in nuclease-free water. The presence of other ions can interfere with the analysis, particularly the Pico and Small RNA chips. Please indicate your elution or re-suspension media if other than nuclease-free water. 

The Core charges for this service by the chip, using either Nano, Pico or Small RNA chips. Nano and Pico chips evaluate total RNA quality and provide a RIN for quality control. Small RNA chips provide separation and analysis of nucleic acids below 150nt, with a final calculation of % miRNA. Sample concentration requirements vary with the type of chip used. Concentration measurement and dilution charges, as needed, are charged per sample.

 Order Submissions

All orders are handled through the NUcore submission system. Core technicians will gladly show you how to submit orders in NUcore if you are unfamiliar with the system. Please follow the directions below to submit samples through NUcore:

1. Go to https://nucore.northwestern.edu/facilities
2. Click on "Login" at the top right-hand side of the page
3. Enter your NetID and password
4. Click on "NUSeq"
5. Click on the link for the service you want (Example: Bioanalyzer - Quality Control Nanochip)
6. Click "Add to Cart"
7. Select the payment source (chartstring number) and click "Continue"
8. Enter the quantity and click "Update"
9. Fill out and upload the completed order form
10. If your order is complete, click on "Purchase", otherwise click on the "Home" tab on the top left-hand side of the page and repeat Steps 4 through 10

 Sample Submission

Please label each sample individually with a barcode label able to withstand -80C temperatures. There are several ways you may send your samples to the Core. Please label each sample individually with a barcode label able to withstand -80C temperatures. If you do not have a barcoded label, please ensure that each sample has a label that is legible and firmly affixed to the sample.

Please freeze samples prior to packing, and ship with sufficient dry ice to ensure they remain frozen. This is to avoid the possibility of cross-contamination or degradation. We cannot accept samples for any study that have thawed or were not shipped frozen.

We recommend that you completely fill the shipping container with dry ice to minimize air space. We also recommend that you pack samples in cardboard freezer boxes placed in large plastic bags to protect samples from dry ice, and use dry ice pellets rather than blocks to avoid damage during shipment.

Include a packing list containing sample IDs, sample type, cell count (if applicable) and box number and position. Please forward an electronic version of this packing list as well so we can have a copy for our records.

There are several ways you may send your samples to the core:

If you are located on the Northwestern University Chicago campus:

Bring your samples directly to the facility:

300 E. Superior St.
Tarry 2-770
Chicago, IL 60611

If you are on Northwestern University's Evanston campus:

Drop off your samples at the Molecular Biosciences Administration office (office location below) to be mailed to our facility. Please label the envelope with your name and the number of reactions.

Department of Molecular Biosciences Administrative Office
Hogan 2100
2205 Tech Dr.
Evanston, IL 60208

The couriers pick up the samples every morning and we receive them in the afternoon.

If you are not located on Northwestern University's campus:

Please send your samples through an independent carrier such as FedEdx or UPS.

Our mailing address:

NUSeq Core
300 E. Superior St.
Tarry 2-770
Chicago, IL 60611

Prior to shipping, please contact a technician to schedule delivery. At the time of shipping, please send an email notification with your express mail tracking number. This will allow us to watch for your shipment. We prefer that samples are sent overnight on Monday or Tuesday so that we can guarantee someone is here to accept them. We will notify you when your shipment is received.

 Turnaround Time

Results are generally delivered within one to two business days.

 Results

Results will be delivered as a PDF file with the quality of their samples, including an electropherogram, gel image, and the samples' RIN's (RNA Integrity Numbers).

All electronic data produced by the NUSeq Core Facility is stored on servers for one year from the date it is made available to customers. Electronic data includes sample, project, and results data files, such as .xsq, .xad, .xls, .txt, .tif, or .jpg files. After the one year retention period, the data will be deleted from the servers. If you have questions about our data retention policy or need to request an additional copy of your data within the one year retention period, please contact nuseq@northwestern.edu.

 Sample Disposal

The NUSeq Core retains submitted samples for two weeks following the completion of a project. If you would like the remainder of any sample to be returned at the completion of the project, please notify the core technicians when you submit your samples and they will be marked for return. Please collect the samples from the core within two weeks of receiving your results. After that time, the samples will be disposed of. The core will not send reminders prior to disposing of the samples.

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