- The GeneChip™ Human Exon 1.0 ST Array, developed by Affymetrix (now part of Thermo Fisher Scientific), is a high-resolution microarray platform designed for comprehensive analysis of the human transcriptome at the exon level.
- Unlike traditional gene expression arrays that measure transcript abundance using probes localized to the 3′ end of mRNAs, this array uses a “whole-transcript” (WT) design, incorporating probe sets distributed across every known and predicted exon of each gene. This enables researchers to assess both overall gene expression and alternative splicing events in a single experiment.
- Each Human Exon 1.0 ST Array contains over 5 million probes, representing more than 1 million exon clusters derived from curated databases such as RefSeq, Ensembl, and GenBank, as well as computationally predicted exons. By targeting multiple regions of each transcript, the array provides more accurate and biologically relevant expression data, especially for genes with multiple isoforms. This whole-transcript coverage allows for the detection of subtle expression changes and splicing variations that may not be evident in traditional arrays.
- The array’s design includes both core probe sets (targeting well-annotated exons), extended probe sets (targeting exons with limited annotation), and full probe sets (including computationally predicted exons). This layered annotation enables researchers to tailor their analysis depending on the desired level of confidence and biological novelty.
- The platform is compatible with the WT Expression (Sense Target) Labeling Assay, which generates labeled cDNA from total RNA, ensuring representation of the entire transcript rather than just polyadenylated 3′ ends. Hybridized arrays are scanned with high-resolution scanners, and the resulting data are analyzed using Affymetrix Expression Console or third-party bioinformatics tools to evaluate both gene- and exon-level expression.
- The GeneChip Human Exon 1.0 ST Array has been widely used in studies of gene regulation, disease mechanisms (e.g., cancer, neurological disorders), and biomarker discovery, where alternative splicing plays a significant role. Its ability to uncover transcript diversity with high sensitivity makes it a powerful tool for transcriptomic research, particularly in contexts where isoform-specific expression changes are biologically significant.
