HiCEP workflowEnlarge Image
Figure 1:HiCEP workflow, click to enlarge.

The HiCEP method is an amplified fragment length polymorphism (AFLP)-based gene expression profiling method that requires no prior sequence information and has a reduced rate of false positives and a high degree of detection of both coding and non-coding transcripts.

Whole transcriptome expression profiling is historically performed using hybridization-based microarray methods. There are a number of limitations to microarray-based approaches such as low sensitivity and specificity, poor dynamic range, as well as a need for prior sequence information. The HiCEP method was developed to address the shortcomings in gene expression profiling and provide a sensitive method for detecting a large proportion of transcripts in both known and unknown genes, with a low false positive rate.

Step-by-Step Guide to High Coverage Gene Expression Profiling

PCR Kit

Amplify the DNA region of interest.

Recommended Products:

Fragment Analysis sizing graph image.

Add aliquot of PCR product to size standard and Hi-Di Formamide mix; heat denature and proceed with electrophoresis.

Recommended Products: Prepare Sample for Analysis

Sizing Information

To learn more about our GeneScan Size standards used in sizing experiments please see our table below.

When DNA fragments are labeled with: Choose a size standards labeled with: Recommended Size Standard Possible Applications Other Kits and Products
dR110, dR6G, dTAMRA™, dROX (Dye Set DS-02 - Filter E5) LIZ®
GeneScan™ 120 LIZ® Size Standard
GeneScan™ 600 LIZ Size Standard v2.0
SNaPshot®
Microsatellite, LOH, ISSR, Chimerism, ISSR, RFLP, T-RFLP, MSMSA
SNaPshot® primer focus kits
Custom Labeled Primer
5-FAM™, HEX™, NED™ (Dye Set DS-30 - Filter D) ROX™ GeneScan™ 500 ROX™ Size Standard Custom Fragment Analysis Custom Labeled Primer
6-FAM™, VIC®, NED™ (Dye Set DS-31 - Filter D**) ROX™ GeneScan™ 500 ROX™ Size Standard

Custom Fragment Analysis

Custom Labeled Primer
5-FAM™, JOE, NED™ (Dye Set DS-32 - Filter F) ROX™ GeneScan™ 500 ROX™ Size Standard
Microsatellite (Forensic)
AFLP
AmpFℓSTR® Kits,
Plant/Microbial AFLP Kits®
6-FAM™, VIC®, NED™, PET® (Dye Set DS-33 - Filter G5) LIZ® GeneScan™ 600 LIZ Size Standard v2.0
Microsatellite (Forensic)
Custom Fragment Analysis
AmpFℓSTR® Kits,
Custom Labeled Primer

Analyze the HiCEP profile.

Which Data Analysis Software Is Right for You?

Highlighted products for High Coverage Gene Expression Profiling:

Verti Thermal Cycler

3500 Series Genetic Analyzers

GeneMapper® Software