|
| Status |
Public on Aug 20, 2015 |
| Title |
Early stage lung squamous cell carcinoma sample Eu36_Nsp |
| Sample type |
genomic |
| |
|
| Source name |
Early stage lung squamous cell carcinoma sample
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Lung
cell type: Lung squamous cell carcinoma
age: 65
gender: Male
tumor stage: IA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extrated from a minimum area of 20 mm2 from microdissected frozen tissue sections (10 μm) using the QIAamp DNA Micro Kit
|
| Label |
Biotin
|
| Label protocol |
500 ng of DNA were separately digested with Nsp I and Sty I restriction enzymes. After adaptors ligation, DNA was amplified in a GeneAmp PCR System 9700 using the TITANIUM DNA Amplification Kit. Following amplification, DNA was fragmented with DNAse I and subsequently biotin end-labeled.
|
| |
|
| Hybridization protocol |
Labeled samples were applied to microarrays and hybridized during 18 h at 49 0C in the hybridization oven
|
| Scan protocol |
The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
|
| Description |
Hybridized to 250K_Nsp
|
| Data processing |
Copy number normalization, to produce log2ratios for individual SNPs was performed using ACNE and NSA R packages. Tumor purity was estimated for each patient using GPHMM software. Circular Binary Segmentation was applied using DNAcopy R package on log2ratio data. Segmented log2ratio was adjusted by estimated tumor purity.
Log2ratio segments may fall within the same gene for a given sample. To solve this problem, a single value was assigned to each gene. A weighted median was performed to the log2ratio values of the segments within the analyzed gene, where the weights correspond to the length of the corresponding segments within the gene.
The Ensembl 54 reference gene set was used (http://may2009.archive.ensembl.org/)
Segmented log2ratio adjusted by tumor purity and summarized by gene (according to Ensembl 54 gene annotation)
|
| |
|
| Submission date |
Aug 19, 2015 |
| Last update date |
Aug 20, 2015 |
| Contact name |
Angel Rubio |
| E-mail(s) |
arubio@ceit.es
|
| Organization name |
CEIT
|
| Department |
Bioinformatics
|
| Street address |
Paseo Mikeletegi, Nº 48
|
| City |
San Sebastian |
| State/province |
GUIPÚZCOA |
| ZIP/Postal code |
20009 |
| Country |
Spain |
| |
|
| Platform ID |
GPL3718 |
| Series (2) |
| GSE72192 |
Combined clinical and genomic signatures for the prognosis of early stage non-small cell lung cancer based on gene copy number alterations [Affymetrix] |
| GSE72195 |
Combined clinical and genomic signatures for the prognosis of early stage non-small cell lung cancer based on gene copy number alterations |
|
