NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1598953 Query DataSets for GSM1598953
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

Data table header descriptions
ID_REF
VALUE Log2 RMA signal.

Data table
ID_REF VALUE
TC01000001.hg.1 5.9
TC01000002.hg.1 5.81
TC01000003.hg.1 3.77
TC01000004.hg.1 6.6
TC01000005.hg.1 8.13
TC01000006.hg.1 9.79
TC01000007.hg.1 10.38
TC01000008.hg.1 5.81
TC01000009.hg.1 3.16
TC01000010.hg.1 3.54
TC01000011.hg.1 5.73
TC01000012.hg.1 4.87
TC01000013.hg.1 9.56
TC01000014.hg.1 6.17
TC01000015.hg.1 5.15
TC01000016.hg.1 5.32
TC01000017.hg.1 6.45
TC01000018.hg.1 6.32
TC01000019.hg.1 6.21
TC01000020.hg.1 7.54

Total number of rows: 70523

Table truncated, full table size 1448 Kbytes.




Supplementary file Size Download File type/resource
GSM1598953_3769_14682_44082_pre-1243_Human-Transcriptome-Array-2.0.CEL.gz 22.0 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap