human neuroblastoma tissue RNA Patient characteristics: Female, 13 months old, stage III unfavorable type neuroblastoma having developed in the adrenal gland.
Biomaterial provider
Clinical sample, Hiroshima University Hospital
Treatment protocol
At surgery, right adrenal tumor and lymph node metastasis were resected. Then, small peccieces of primary tumor was picked up and frozen immediately until use.
Growth protocol
none
Extracted molecule
total RNA
Extraction protocol
Total RNA was extracted from tissue specimen using RNA isolation kit according to the manufacturer’s instructions (Stratagene, Agilent techonology, Santa Clara , CA) and the quality of the RNA was checked using an Agilent Technologies 2100 Bioanalyzer (Agilent, Palo Alto, CA).
Label
biotin
Label protocol
2 μg of total RNA was used for first strand synthesis and 10 μg of cRNA was used for hybridization using the CodeLinkTM Expression Assay Reagent Kit. Conversion of double stranded cDNA into biotin-labeled cRNA was accomplished using the First and Second Strand cDNA Synthesis Kit and In Vitro Transcription (IVT) Kit (BE Healthcare) according to the manufacturer’s instructions.
Hybridization protocol
The protocol and conditions used during hybridization, blocking and washing are provided in the following source: CodeLinkTM User Protocols.
Scan protocol
The CodeLink microarray was scanned using an Agilent™ DNA Microarray Scanner and processed using CodeLink™ System Software for Analysis.
Description
Three commercially available single-color oligonucleotide microarray platforms for profiling gene expression - CodeLinkTM Human Whole Genome Bioarray (~55,000 transcripts, GE Healthcare, Tokyo, Japan), Affymetrix GeneChipTM Human Genome U133 Plus 2.0 array (~47,000 transcripts, Affymetrix, Santa Clara, CA), and Agilent Whole Human Genome Oligo Microarray (~41,000 transcripts, Agilent Technologies, Tokyo, Japan), were compared using the same RNA sample extracted from a human neuroblastoma tissue sample.
Data processing
Data processing Data were processed using functional ‘ON/OFF’ state of a gene
