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.
Our publication about custom CDF:
Evolving Gene/Transcript Definitions Significantly Alter the Interpretation of GeneChip Data
M. Dai, P. Wang, A.D. Boyd, G. Kostov, B. Athey, E. G. Jones, W. E. Bunney, R. M. Myers, T. P. Speed, H. Akil, S. J. Watson, F. Meng
Nucleic Acid Research. 2005; 33(20), e175
Systematic analysis of the impact of custom CDF on GeneChip data analysis:
The effect of GeneChip gene definitions on the microarray study of cancers
Lu X, and Zhang X
Bioessays. 2006; 28(7):739-46
Improved precision and accuracy for microarrays using updated probe set definitions
Rickard Sandberg and Ola Larsson
BMC Bioinformatics. 2007; 8:48
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.