The Covance Genomics Laboratory (CGL) Process
Gene expression analysis follows a quality-controlled process to ensure robust, consistent data. Follow a sample through our laboratory from tissue homogenization to expression analysis results. More detailed explanations are available through the sub-pages.
Tissue Homogenization
Scientists send samples to CGL in the form of tissue, cells, or even plaque. The sample is homogenized to extract RNA.
» Learn more about Tissue Homogenization
Sample QC
Incoming samples or extracted samples are evaluated before processing for amplification.
» Learn more
RNA Extraction
mRNA is amplified and labelled using a number of different protocols depending the assay platform and experimental design. CGL offers protocols for total RNA input levels of 1 ng - 2 ug, as well as for FFPET and whole blood samples.
» Read about the RNA Extraction process at CGL
Amplification
RNA is amplified through Reverse Transcription (RT) and in vitro transcription (IVT). Probes are added to detect the subtle changes in gene regulation. CGL offers several different types of amplification based on sample requirements.
» Find out about CGL Amplification
In Process QC
Samples are monitoried during amplification and other downstream processes.
» Learn more
Hybridization
The sample is added to the microarray, where sequences of the RNA hybridize or join to the 44,000 complementary sequences on the microarray. The microarrays are then dried in nitrogen chambers and any unmatched sequences are rinsed off.
» Learn more about Hybridization
Profile QC
The accuracy of the hybridization data is measured.
Project QC and Data Analysis
Our Quality assurance and analytics team analyzes the result data for millions of SNPs per array, as well as providing the copy number variants, call rate analysis, and overall sample and project reports. Our standard data deliverables include .cel files and a final report that correlates sample barcode with the array barcode and provides a performance analysis of the microarray data. Data will be provided via FTP or can be shipped on a memory storage device.
Value-added services are available, based on the client’s preferences and overall scientific objectives. This can include a detailed project level analysis, such as applying of expression algorithms and error models, identifying artifacts, performing inferential analyses, and generating analysis-ready data using commercial and public tools such as R, Spotfire, SAS, Matlab, or Resolver.