Total RNA was isolated using miRNAeasy kits (Qiagen, Valencia, CA). RNA concentrations were calculated using a Nanodrop ND-1000 spectrophotometer (Nanodrop Technologies, Rockland, DE) and RNA integrity (RIN) was evaluated using the RNA 6000 PicoAssay (Agilent Technologies, Santa Clara, CA). RNA samples with RIN values of <4.0 were subjected to an RNA cleanup step using the mRNAeasy kit (Qiagen, Valencia, CA).
Label
biotin
Label protocol
Affymetrix SOP
Hybridization protocol
Affymetrix SOP
Scan protocol
Affymetrix GeneChip scanner
Data processing
Data were processed using Affymetrix Power Tools (APT). Robust Multi-array Average (RMA) was used to generate normalized gene-level signal intensity estimates. Only core probesets uniquely mapped to the genome were used.
Gene Expression Profiling of Ewing Sarcoma Tumors Reveals the Prognostic Importance of Tumor-Stromal Interactions: A Report from the Children's Oncology Group
Data table header descriptions
ID_REF
VALUE
Quantile normalized gene level expression values from APT
