|
| Status |
Public on Oct 04, 2009 |
| Title |
Lung squamous cell carcinoma sample 15T |
| Sample type |
genomic |
| |
|
| Source name |
Lung squamous cell carcinoma sample 15T
|
| Organism |
Homo sapiens |
| Characteristics |
cancer type: Non-small cell lung cancer
cancer sub-type: Squamous cell carcinoma
tumor type: primary
|
| Growth protocol |
Cell lines were grown according to standard conditions.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from samples using the Qiagen Puregene kit and quantitated with PicoGreen.
|
| Label |
Biotin
|
| Label protocol |
As per manufacturer (Affymetrix)
|
| |
|
| Hybridization protocol |
DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
|
| Scan protocol |
Arrays were scanned using the Gene Chip Scanner 3000.
|
| Description |
Hybridized to 250K_Sty
|
| Data processing |
DNA from tumor samples were processed and hybridized to Affymetrix StyI 250K SNP arrays using standard protocols. Normalization of the individual tumor (or tumor cell)'s SNP array data was performed with a newly developed method termed Tangent normalization (full desciption pending in Getz, et al; manuscript in preparation). For Tangent normalization, SNP array data from as large a pool of non-cancerous normal samples as possible are obtained. In this analysis, we used data from >1100 normal samples. The SNP data from these normals are used to generate a high-dimensional hyperplane that represents all linear combinations of the signal intensities seen in the normal samples; we then project each tumor sample onto this plane to find the 'hypothetical reference' sample that most closely matches that tumor, and use this reference point to infer the copy number. After the copy-number are inferred from this new technique, we use the GLAD segmentation/smoothing algorithm to further process the data.
|
| |
|
| Submission date |
Sep 03, 2009 |
| Last update date |
Sep 28, 2009 |
| Contact name |
Adam Joel Bass |
| E-mail(s) |
adam_bass@dfci.harvard.edu
|
| Organization name |
Dana-Farber Cancer Institute
|
| Street address |
44 Binney Street
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL3720 |
| Series (1) |
| GSE17958 |
Affymetrix SNP array data for 47 lung squamous cell carcinoma and 40 esophageal squamous cell carcinoma samples. |
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