|
| Status |
Public on Jun 19, 2014 |
| Title |
lung_30 |
| Sample type |
RNA |
| |
|
| Source name |
Right Upper Lobe
|
| Organism |
Homo sapiens |
| Characteristics |
gender: M
histology: 869. Squamous Cell Carcinoma, NOS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples are processed in parallel in 96-well plates to minimize potential variation. Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification. Isolated total RNA samples were assayed for quality (Agilent Bioanalyzer) and yield (Ribogreen) metrics prior to amplification.
|
| Label |
biotin
|
| Label protocol |
Samples were amplified and labeled using a custom automated version of the NuGEN Ovation v2 with WB (whole blood) reagents protocol (using Ribo-SPIA amplification). The labeled molecules are biotinylated-cRNA. Sample amplification and labeling were performed by LabCorp Clinical Trials-Genomic Services in Seattle, Washington.
|
| |
|
| Hybridization protocol |
GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques. Arrays are hybridized for 18 hours at 45C with vigorous mixing. Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed. Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.
|
| Scan protocol |
Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.
|
| Data processing |
Raw CEL files were normalized by RMA algorithm as implemented in the justRMA function in Bioconductor/R with default parameters.
|
| |
|
| Submission date |
Jun 19, 2014 |
| Last update date |
Jun 19, 2014 |
| Contact name |
Patrick Grossmann |
| E-mail(s) |
PATRICK@JIMMY.HARVARD.EDU
|
| Organization name |
Dana-Farber Canacer Institute
|
| Department |
Radiation Oncology
|
| Lab |
Aerts Lab
|
| Street address |
450 Brookline Ave
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL15048 |
| Series (1) |
| GSE58661 |
89 NSCLC patients with gene expression profiles and matching CT imaging data available at TCIA. |
|
