RNA Extraction and Quality Control
RNA extraction and quality control of the extracted nucleic acid is crucial for sequencing, microarray analysis, or other genomic technologies. The CGF has established standard operating procedures for extractions to minimize the degradation and contamination of precious patient samples. At the CGF we specialize in extraction from paraffin embedded tissue with and without slide dissection.
The CGF offers RNA extraction services from a variety of sample types such as:
- Frozen tissue
- Formalin Fixed Paraffin Embedded Tissue scrolls
- Formalin Fixed Paraffin Embedded Tissue slides
- FFPE slides with micro and macro-dissection
For other sample types not listed, please contact the CGF.
The CGF offers the following RNA quality analysis services:
- Nucleic acid quantitation via the NanoDrop ND1000 and the Qubit Fluorometer
- Nucleic acid quality assessment via the Agilent Bioanalyzer
Sample Submission Requirements
Frozen or FFPE tissue for RNA extraction may be requested through the Hillman Tissue and Research Pathology Services (TARPS) or provided by the individual researcher.
For researchers who are collecting samples on their own, we suggest a few guidelines to limit RNA degradation and ensure sample quality. All samples submitted to the lab for extraction and downstream assays should be handled in one of the following ways at the time of collection:
- Fresh tissue should be ash frozen in 2.0 mL round bottom tubes or Nunc tubes in LN2 or dry-ice and maintained at -80°C until submitted to the CGF. Cells should be pelleted in 1.5-2.0 mL tubes, all supernatant removed, and then flash frozen in LN2 and maintained at -80°C until submitted to the CGF.
- FFPET samples may be submitted in one of two ways:
- Submit (10) 10-micron scrolls in round bottom 2.0 mL microcentrifuge tubes
- Submit (10) 10-micron blank slides for FFPET extraction. The CGF can perform micro/macro-dissection of the area of interest from the FFPET slide if the researcher provides an accompanying H&E slide. If this service is requested, we suggest that the researcher contact the CGF staff member prior to submitting samples.
Once samples have been extracted, they will be assessed for quality, quantity, and concentration. The CGF will provide a detailed QA/QC report to the researcher.
RNA Services: QA/QC
The CGF offers DNA quality analysis services using the following instruments: NanoDrop ND1000, Qubit Fluorometer, and the Agilent Bioanalyzer 2100.
Researchers can submit the following samples for RNA QA/QC:
- Total RNA, mRNA
- PCR product
- Sequencing libraries
- Custom request
Technology and Equipment
The Agilent 2100 Bioanalyzer is a microfluidics-based platform for sizing, quantification and quality control of DNA, RNA, proteins, and cells on a single platform.
The Nanodrop (Thermo Scientific) is a micro-Volume UV-Vis spectrophotometer for nucleic acid and protein quantitation that allows for sample volumes as small as 0.5 μL. It offers:
Life Technologies Qubit Fluorometer
The Qubit® 3.0 Fluorometer utilizes specifically designed fluorometric technology using Molecular Probes® dyes. These fluorescent dyes emit signals ONLY when bound to specific target molecules, even in the presence of free nucleotides or degraded nucleic acids. Qubit® fluorometric quantitation provides the most specific and sensitive DNA and RNA quantitation available, even at low concentrations.
For pricing information, please contact Maureen Lyons.