Isolation of nucleic acids from diverse biospecimen samples
About
The DNA/RNA purification core features instruments that allow extraction of nucleic acids from a larger variety of tissues, at a higher throughput, and at a more competitive price.
The DNA/RNA purification core offers nucleic acid extraction from whole blood (large or small volume), buffy, buffy coat, saliva, buccal swab, blood cards, plasma, cultured cells, or tissue. DNA extraction is available from all of these biological samples, and RNA extraction is available from most as well.
We also offer DNA and RNA QC, low and medium throughput SNP genotyping (1-30 SNPs), APOE genotyping, Sanger sequencing, sample storage, DNA/RNA normalization, and DNA/RNA plating for transfer to GTAC@MGI (or another service provider) for genotyping or sequencing.
For a complete list of services and current prices please check the Current Fee Schedule
Location
4444 Forest Park Blvd
Suite 5120
St. Louis, MO 63108-2212
Guidelines for submitting samples
As of January 1, 2017 we are no longer accepting blood samples in glass tubes due to safety issues related to tube breakage. Plastic collection tubes will be required for all samples. Please see below for guidelines.
Please contact Kristy Bergmann and fill out the Sample submission form before dropping off samples.
General notes
For best results, freshly drawn blood should be stored at 4°C for less than 4 days, or should be frozen at -80°C on the day of collection if possible. Samples should be submitted to the core within 1 – 4 days after collection for optimal results. Samples at can be also storage at -20°C but for no more than 3-6 months.
All sample tubes should be labeled with a unique sample identifier, the PI name, and the date collected.
DNA/RNA will be returned in 2D barcodes tubes, unless a different tube is requested in advance.
Nanodrop information will be provided for all samples extracted by the Hope Center DNA/RNA core.
Whole Blood and buffy
Blood samples should be collected in PLASTIC TUBES, preferably EDTA (e.g. BD Vacutainer #366643 purple cap tubes). Collection in ACD (citrate, yellow cap tubes) is also acceptable. Please DO NOT USE GREEN CAP (Heparin) Tubes. Other plastic blood collection tubes are acceptable provided they meet the guidelines above.
Tissue and cell pellets
Tissue samples and cell pellets should be snap frozen on dry ice and stored at -80°C. Samples should never be stored at -20°C as they quickly degrade.
Samples stored for more than 1 year or at less than -80°C may result in lower yield and quality of DNA. Multiple freeze/thaws will also affect DNA yield and quality.
Resources
Large volume DNA samples (1 – 10 ml) are extracted on the Autogen FlexSTAR+ using proven Flexigene chemistry, a salt precipitation method that removes protein contaminants and enzyme inhibitors. The FlexSTAR+ platform is capable of high-throughput purification from large volume samples (1 – 10 ml) in ~ 4 hours (30 samples for 1-5 mL or 15 samples for 6-10 mL.)
DNA or RNA are extracted from small volume samples (generally < 500mL) using magnetic bead-based purification chemistry. The Maxwell RSC 48 can process a large variety of input sources (blood, buffy, saliva, blood cards, tissue, buccal swab, plasma, CSF, cultured cells, and others).
The QIAgility and Biomek FXP liquid handling workstations enables high-precision pipetting, eliminating manual pipetting errors and ensuring consistent, reproducible results. The Biomek FXP includes a multichannel (96 head) and a Span-8 head. This increased efficiency and flexibility all allow high-throughput protocols.
The TapeStation 4200 system is an established automated electrophoresis tool for DNA and RNA sample quality control. DNA and RNA quality and quantity are assessed with the TapeStation 4200, which is able to run up to 96 samples in one run and provides both concentration and quality metrics (DIN or RIN). Fully automated sample processing enables the unattended analysis of size, concentration and integrity. The TapeStation system provides a complete solution for true end-to-end sample quality control within any next-generation sequencing (NGS) or Biobank workflow.
The 3500 Genetic Analyzer is an 8-capillary sequencing instrument specifically designed to support the demanding performance needs of validated and process controlled environments, while retaining the unsurpassed application versatility that life science researchers expect. The 3500 Series Data Collection Software supports sequencing and fragment analysis, and integrates seamlessly with downstream software for secondary analysis of genetic data.
The Life Technology StepOnePlus Real Time PCR machine (96-well plate); a QuantStudio 12K Real Time PCR machine (384-well plate) are used for qPCR, allele specific gene expression, and SNP genotyping.
The MassARRAY instrument allows genotyping from 1- 32 SNPs. This can be used to genotype specific custom SNP sets, or pre-made set for association studies or DNA fingerprinting. The MassARRAY genotyping technology is based upon primer extension using allele-specific mixtures of dNTPs and ddNTPs with mass spectrometric analysis of the products. The iPLEX Gold platform is designed to genotype multiplex pools up to 32 SNPs per well. A custom assay is designed for each pool of SNPs to be genotyped. In general, 85-99% of SNPs will be able to have a successful genotyping assay designed.
Contact Information
- Core Director: Carlos Cruchaga
- Research Technician: Kristy Bergmann
Inquiries and sample submission
For inquiries about a new project, contact Core Director Carlos Cruchaga.
To submit samples, please complete a sample submission form and forward to Kristy Bergmann.
NOTE: Users must provide a cost center when samples are submitted.
User fees
Charges for Hope Center investigators are subsidized by the Hope Center. This subsidy will apply only if the billing PI is a Hope Center faculty member.
Acknowledging the Core
Please acknowledge the Core in manuscripts as well as posters and talks. Suggested language: “This work was supported by the Hope Center DNA/RNA Purification Core at Washington University School of Medicine.”
ICTS Funding Option
Hope Center Core users may be eligible to apply for a Just-in-Time (JIT) award from the Washington University Institute of Clinical and Translational Sciences (ICTS). Faculty members without established funding for their projects are encouraged to apply for JIT funding through the ICTS. Visit the ICTS JIT webpage for additional details.