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Microarray Platform: Affymetrix human U133A chip

Summary: Fanconi Anemia (FA) is an inherited disorder associated with hypoplastic bone marrow failure, developmental anomalies, and a high relative risk of acute myelogenous leukemia and epithelial malignancies in children and young adults.

The FA Transcriptome Consortium, supported by the Fanconi Anemia Research Fund, in October 2006 publicly released this gene expression data from two sets of samples: 20 aplastic Fanconi marrows (with no clonal cytogenetic defects) and bone marrow samples from 11 normal volunteers. RNA was prepared in the participating institutions and shipped to Portland on dry ice.

Complementary DNA and cRNA was prepared, cRNA fragments labeled for use as targets of the probes in the human U133A Affymetrix chip. MAS 5.0 was utilized to process images, quantify signals, adjust background, and to scale the data. The resulting Affymetrix CEL files were then uploaded into GeneSifter using RMA.