|
| Status |
Public on Oct 31, 2015 |
| Title |
Patient-29.pre |
| Sample type |
RNA |
| |
|
| Source name |
breast cancer
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: breast cancer
dose: none
pre or post treatment: pre
|
| Treatment protocol |
Formalin fixed and paraffin-embedded (FFPE) samples were obtained at the time of diagnosis. Patients then received a single large dose of radiation to the intact tumor and proceeded to surgical resection within 10 days of treatment. A second post-radiation sample was obtained at the time of surgical excision.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
FFPE RNA extraction and labeling was performed using the RNeasy FFPE kit from Qiagen, and the SensationPlus™ FFPE Amplification and Labeling Kit (Affymetrix, Inc. catalog # 902312). All total RNA samples were assessed for quality using a NanoDrop ND8000 Spectrophotometer for absorbance ratios, and the Agilent Bioanalyzer 2100 for RIN scores. Whole transcriptome expression analysis was evaluated with HTA 2.0 arrays (Affymetrix, Inc. catalog # 902162).
|
| Label |
biotin
|
| Label protocol |
SensationPlus™ FFPE Amplification and Labeling Kit (Affymetrix, Inc. catalog # 902312).
|
| |
|
| Hybridization protocol |
Hybridization of samples to Affymetrix GeneChip arrays was performed according to Affymetrix manual instructions .
|
| Scan protocol |
Scanning of Affymetrix GeneChip arrays was performed according to the Affmetrix manual instructions.
|
| Description |
Patients with biologically favorable early stage breast cancer participating in an IRB approved phase I dose-escalation preoperative radiotherapy protocol.
|
| Data processing |
Gene level expression estimates were obtained with Affymetrix Expression Console software (v.1.3) using RMA-Sketch workflow. Differential expression for paired samples was evaluated using the Bioconductor limma package with correction for multiple comparisons. Genes with FDR adjusted p-values (q-values) less than 0.05 were selected as differentially expressed in response to radiation. This set of genes was then tested for radiation dose effect using linear regression of the log2 fold change over dosage received. Those genes with regression p-values less than 0.0005 and q-values less than 0.25 were selected as having dose effect. Gene set analysis (GSA) was performed with the R package GSA using “two class paired” problem type and 100,000 permutations to estimate false discovery rates. The gene set collection used is “all GO (gene ontology) gene sets” which contains 1454 gene sets in total.
|
| |
|
| Submission date |
Feb 02, 2015 |
| Last update date |
Oct 31, 2015 |
| Contact name |
Wei Chen |
| Organization name |
Duke University
|
| Department |
Center for Genomic and Computational Biology
|
| Street address |
101 Science Drive
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27708 |
| Country |
USA |
| |
|
| Platform ID |
GPL17586 |
| Series (1) |
| GSE65505 |
Gene expression profiling in response to radiation treatment in human breast cancer |
|
