Oligonucleotide probes on GeneChips are reorganized based on the latest genome and transcriptome information. In addition to custom CDF files for different target definitions, GeneChips and data analysis platforms, we also provide 1) a probe mapping file that matches individual probes in the custom CDF file and the corresponding Affymetrix CDF file; 2) a grouping file that can be used to find all targets (exons, transcripts) represented by the same probe set. The grouping file also contains the probe set spanning range on genome or transcripts to facilitate RT-PCR primer design.

Click here for the detailed description of these CDF files.

Our publication about custom CDF:

Systematic analysis of the impact of custom CDF on GeneChip data analysis:

And some papers that cited our work

We gratefully acknowledge the funding support from the Pritzker Neuropsychiatric Disorders Research Consortium, Janssen Research & Development and Hope For Depression Research Foundation.