Sample Quality Control


The Genomic and RNA Profiling Core Facility makes every effort to ensure that the products and services we provide have been assessed with the most stringent quality control possible. We integrate QC steps in all standard operating procedures and utilize outside products in necessary.

All samples submitted to the GARP by the user must first go through a sample quality check, or SAQC, in order to determine integrity, concentration, and overall quality of the sample. Please see our GSLE information page to find out more about the process involved in a SAQC request.

GARP will accept a single tube to be used in both the Quality Control test and the downstream application (Sequencing or NanoString). Please be sure to add 5-10ul extra to the requirements for RNA/DNA samples to be submitted for Sequencing Library Prep or NanoString. For prepared libraries, users should plan to submit no less than 10-15ul or the entire library sample if possible. If insufficient DNA/RNA is submitted, another aliquot must be submitted from the same identical stock solution without additional manipulation (dilution) as what was provided for the original QC.

Requirements for downstream applications can be found:

Agilent Bioanalyzer RNA Concentration Requirements:

Nano: 25-500 ng/μL
Pico: 200-5,000 pg/μL

RNA Quality Control

We accept the following RNA sample types: total RNA, mRNA, aRNA or cRNA, labeled cRNA, microRNA, RNA-IP. Samples should be diluted with RNase-free water.*

Users must submit at least 5 μL of sample in a 1.5 mL microfuge tube.

Samples are tested for quality assurance on the Agilent 2100 Bioanalyzer and quantitated on the NanoDrop Spectrophotometer.

Users should download Agilent's free viewer software to review results.

DNA Quality Control

We accept the following sample types: Genomic DNA, single stranded cDNA, double stranded cDNA, PCR product.

gDNA samples should be diluted in Nuclease-free water to a concentration of 50-100 ng/μL.* Please submit 5 μL aliquots in 1.5 mL microfuge tubes.

DNA Fragments (ChIP DNA, PCR products or user-prepared libraries) should be diluted to <50ng/μL in 10μL. GARP will quantitate DNA samples on the Qubit Fluorometer, NanoDrop Spectrophotometer, and by qPCR (Illumina libraries) and fragment size on an Agilent 2100 Bioanalyzer DNA Chip. Please submit 10 μL aliquots in 1.5 mL microfuge tubes. For Illumina library QC samples, GARP will save dilutions made during the QC process and use these aliquots to pool and prepare the template for sequencing should the user decide to proceed with sequencing through GARP.

For ChIP-seq users: Please be aware that GARP must see your qPCR data from your samples and positive control from both the post-ChIP processing as well as post-amplification. We cannot pass your SAQC Request without the data. If you did not run a positive control, you (or your PI if you are not the PI) will need to sign-off on your samples. The sign-off releases GARP from any responsibility of inadequate sample or chip performance.

Sample integrity may be tested using either agarose gel electrophoresis (genomic DNA), the Agilent 2100 Bioanalyzer or the Agilent 2200 TapeStation and quantitated on the NanoDrop Spectrophotometer and Pico Green (Qubit Fluorometer). Illumina libraries will additionally be quantitated by qPCR analysis.

Users should download Agilent's free viewer software to review results. Additionally, users may receive files generated by the Agilent TapeStation. Users can download the 2200 TapeStation Analysis software for free from the Agilent website here: 2200 TapeStation Software.

Once samples pass the QC step, they are then available for selection for other services in the GARP using GSLE.

*The GARP is not responsible for proper dilution of user sample. It is the user's responsibility to dilute the samples submitted to the proper concentration. GARP will charge a dilution fee of $15 per sample for all RNA or DNA submitted for quality check not within the proper concentration range.

Notice: Starting July 1, 2013, all DNA QC requests will have an extra fee of $5/sample to account for Qubit measurements.