Agilent 4 44 k whole human genome oligo microarrays

The mRNA expression profiles of tumor samples from Patient 1 and the 50 additional GBM patients were generated using Agilent 4 × 44 K Whole Human Genome Oligo Microarrays (Agilent, USA). The data were normalized using the quantile method of the “limma”^{31 (link)} R package. All of the raw and processed data are available from the GEO database (accession numbers GSE83300 and GSE83301). The raw mRNA expression data and the corresponding clinical information, which was available for 487 GBM samples, were downloaded from the Cancer Genome Atlas (TCGA) database (https://tcga-data.nci.nih.gov/tcga/tcgaHome2.jsp) and processed using the RMA methodology included in the “affy”^{32 (link)} R package.

Sixty GBM samples with OS and PFS information were obtained during surgical resection from Tian Tan Hospital from 2008 to 2010. All donors signed informed consent forms. The use of human tissue samples and the experimental procedures for this study were reviewed and approved by the Ethics Committee of the Cancer Institute and Hospital, Chinese Academy of Medical Sciences.
Total RNA was isolated with Trizol reagent (Invitrogen, CA, USA), and those allocated for microarray detection were purified with an RNeasy kit (Qiagen, MD, USA). RNA was quantitated with ND-1000 UV-VIS Spectrophotometer (NanoDrop Technologies, DE, USA) and the integrity of RNA was assessed using the RNA 6000 Labchip kit in combination with the Agilent 2100 Bioanalyzer (Agilent, CA, USA). Purified total RNA samples were labeled and hybridized to Agilent 4 × 44 K Whole Human Genome Oligo Microarrays according to the manufacturer's instructions.
Furthermore, the raw and processed gene expression data and clinical information of the sixty GBM samples have been deposited in Gene Expression Omnibus (GEO) database with the series accession numbers GSE74187.

RNA samples from five PLC patients were analyzed using the Agilent 4 × 44 K Whole Human Genome Oligo microarrays (Agilent, cat.no G4112A). The labeling, hybridization, and washing were performed according to the manufacturer's instructions. Then, the slides were scanned using an Agilent SureScan Microarray Scanner (G2600D) and extracted with Agilent Feature Extraction Software v10.5.1.1.
The data were normalized using the quantile method from the “limma” R package. The raw and normalized PLC data were submitted to the GEO database with the accession number GSE92528.