There are three major categories of targeted gene expression analysis techniques that the CGI can assist with: qRT-PCR, Targeted RNA-seq and Digital Droplet PCR.
qRT-PCR
Quantitative real-time PCR is used to quantify expression levels of a single or small number of targets in a given RNA sample. The CGI offers both 96 and 384 well qPCR machines (two of each BioRadCFX96 and CFX384 instruments) that can be reserved for use. Users are expected to bring their own reagents/plates specific for their assay.
Target RNA-seq
In targeted RNA-seq, a target enrichment panel allows the user to maximize sequencing depth by focusing on only a portion of transcripts within a sample, such as genes in a specific pathway, fusion genes, or only a subset of sequences. There are currently several commercially available panels for targeted RNA-seq and several vendors offer targeted panel design. If you would like to discuss targeted RNA-seq and supported panels, contact us and we can help guide you in your experimental design.
Digital Droplet PCR
The CGI has a BioRad QX200 Droplet Generator and Reader for use in digital droplet PCR. Assays supported include EvaGreen (SYBR green equivalent for droplet emulsion reactions) or Probe assays for gene expression, copy number variation or mutations (available directly from BioRad with UCONN discounts). It is very important to make sure the preparation of your DNA or cDNA samples uses approved plastics. he BioRad QX200 system and its reagents are very sensitive to micro-debris found in certain plastics and these micro-debris can cause clogs in the channels of the emulsion chip. The following plastics are approved for use on the QX200 system:
Pipette tips validated for our instrument:
- Rainin
- DOT Scientific
Please avoid using:
- ARTips
- USA Scientific Tips
LoBind Eppendorf tubes should be used for your genomic DNA samples or PCR strip tubes from Dot Scientific. If you are unsure about the tips and tubes you are using for sample extraction and storage please call BioRad tech support.