USC

Affymetrix Core

The CHLA Affymetrix core (Genomics Core) provides genomic analyses, predominantly using Affymetrix GeneChips, for:

  1. Whole transcriptome gene expression profiling, for human and mouse, and any other organism for which Affymetrix microarrays are available.
  2. p53 mutation analysis, using Affymetrix p53 GeneChips.
  3. Whole genome high density SNP analyses, using 10K, 100K SNP and 500K arrays.
Gene expression values are confirmed using QPCR (Cephiad, Sybr Green 16 well multiplex PCR device). Currently, up to 48 genes can be run simultaneously, and several fold more in multiplex reactions. In addition, the core provides confirmatory analysis of sequences using an ABI multi-channel capillary electrophoresis DNA sequencer.

The core also provides support for bioinformatics analysis of all the above, using custom software (e.g., Genetrix) developed at USC and provided to all users at no charge. In addition, users are provided with an initial analysis of their data by the core bioinformaticist, Xuan Chen, that includes quality assurance data and basic comparisons. In depth consultation and analysis is available from two PhD faculty level members of the core (e.g., Paul Marjoram, PhD and Jonathan Buckley, MD, PhD).

USC/CHLA MicroArray Core