|
| Status |
Public on Jul 06, 2010 |
| Title |
Matched normal for tumor PT3DD |
| Sample type |
genomic |
| |
|
| Source name |
matched normal DNA
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Matched normal tissue
disease status: normal
sample id: PT3DD
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from cyromoled-macrodissected tumor samples and from blood or normal adjacent tissue and digested with the StyI restriction enzyme
|
| Label |
Cy3 and Cy5
|
| Label protocol |
PCR projects, after pooling, concentration, and fragmentation with Dnase I were labeled and denatured as per manufacturer's instructions with Bioprime Array CHG labeling kit (Invitrogen) using Cy3/Cy5.
|
| |
|
| Hybridization protocol |
Per manufacturer's instructions
|
| Scan protocol |
After hybridization, arrays were washed with Affymetrix fluidics station and scanned with the Gene Chip Scanner 3000 7G and Affymetrix Genotyping Tools Version 2.0
|
| Description |
Hybridized to 250K_Sty
|
| Data processing |
Signal instensities were were quantified and normalized with the Affymetrix Chromosomal Copy Number Analysis Tool (CNAT 4.0, 1.5.6_v3.1) and copy number was converted to tumor-to-normal log2 ratios using the algorithm described in Taylor BS, et al PLoS ONE 2008; 3(9):e3179. Cell line signal intensities were normalized to a baseline array with median intensity and quantile normalization in GenePattern based on the dChipSNP algorithm. SNP-level inteisities were obtained for these using the model-based PM/MM method. Data from each were compared to data from 1800 normal datasets, and the 5 normal samples with noise profiles most similar to each cell line were used to determine log2 ratios at each SNP locus.
The normalized tumor/normal ratio data described above are presented in the Sample data tables of the Tumor sample (normal Samples therefore do not have data tables). The matrix of ratio data is also available as a text file on the Series record.
|
| |
|
| Submission date |
Mar 30, 2010 |
| Last update date |
Jul 06, 2010 |
| Contact name |
Barry Stephen Taylor |
| Organization name |
Memorial Sloan-Kettering Cancer Center
|
| Street address |
1275 York Avenue, Box #460
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL3720 |
| Series (2) |
| GSE21123 |
Affymetrix SNP array data for soft tissue sarcoma samples |
| GSE21124 |
Subtype-specific genomic alterations define new targets for soft tissue sarcoma therapy |
|
