RNA and DNA quality control
Sample quality is critical in genomic experiments. Performing sample QC before, during and after library preparation delivers valuable information that is vital to the overall success of the sequencing results. At GCF, we place high value on quality control at every stage of our process to ensure delivery of high-quality data.
DNA and RNA quality control
At GCF, we place high value on quality control at every stage of our process to ensure delivery of high-quality data.
- Input sample QC: By determining the input sample (DNA/RNA) quality before library preparation provide the necessary information to adapt library preparation protocols according to the sample’s concentration, quality and integrity
- Intermediate sample QC: Evaluating the quality of intermediate products during library preparation ensures that only samples meeting the required criteria are selected
- Final library QC: A quality check of the final library before sequencing helps sample normalization and to avoid potential sequencing over-amplification artifacts that may occur during PCR amplification.
GCF provides quality control service using the Agilent Tapestation system for both DNA and RNA and quantification using the Qubit assays or NanoDrop.
GCF provides quality control service using the Agilent Tapestation system for both DNA and RNA and quantification using the Qubit assays or NanoDrop.
RNA/DNA sample preparation and QC
Important to know about RNA/DNA Sample Preparation and Quality Control
It is important that users provide DNA or RNA samples with required quality and quantity.
Here are some general guidelines for sample preparation and quality control.
RNA quality check
RNA samples should be free of proteins, DNA, phenol, ethanol and salt.
We recommend RNeasy kit from Qiagen or similar for RNA preparation. If TRIzol based methods are used to extract RNA from tissues, we recommend a cleanup procedure with Qiagen RNeasy mini kit following the phenol extraction.
If possible, DNase treatment should always be performed when extracting RNA for genomic analysis.
RNA quantitation
We recommend Qubit® fluorometric quantitation.
RNA quality assessment
The quality of total RNA samples is the most important factor in RNA-Seq. RNA samples should be quality checked on a Tapestation (or similar system). If there is significant degradation (when RNA Integrity Number, or RIN, is below 7.0), we will request the customer to re-submit total RNA samples of satisfactory quality.
DNA quantitation
We recommend the Qubit® fluorometric quantitation for quick and accurate quantitation. You can also check the OD260/280 ratio using a NanoDrop, this ratio is a indicator of purity and should be between 1.8 -2.0 for a good DNA sample.
Genomic DNA Quality Assessment
DNA samples must not be highly degraded. We recommend quality check on a TapeStation or a 1 % agarose gel. High quality genomic DNA should give a major band of 10-20 kb on the gel.