|
| Status |
Public on Dec 10, 2014 |
| Title |
NSCLC cell line SK-1 nsp [SK-13] |
| Sample type |
genomic |
| |
|
| Source name |
SK-1
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: lung carcinoma cell line
cell line: SK-1
|
| Treatment protocol |
None
|
| Growth protocol |
Cell lines were grown according to standard conditions.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from cell lines, and fresh frozen lung tumors using the Qiagen AllPrep kit. DNA from lung paraffin embedded tumors was obtained using the RecoverAll kit from Ambion. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.
|
| 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 |
The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
|
| Description |
Hybridized to 250K_Sty
|
| Data processing |
The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares. Genomic Smoothing analysis was performed by using the smoothing window of 0 Mb, and inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in CNAT 4.0.1. Circular Binary Segmentation (Ohlsen et al., 2004) was applied using DNAcopy package for R Bioconductor on raw data. Copy number from the parffin embedded tumor DNA was calculated after filtration of the PCR fragments above 800 Bp to account for DNA degradation
primary data description: Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal
|
| |
|
| Submission date |
Oct 16, 2014 |
| Last update date |
Aug 19, 2016 |
| Contact name |
Alfredo Hidalgo-Miranda |
| E-mail(s) |
ahidalgo@inmegen.gob.mx
|
| Phone |
+52-55-53501966
|
| Organization name |
National Institute of Genomic Medicine
|
| Street address |
Periferico Sur 4124, Torre Zafiro II, piso 6
|
| City |
Mexico City |
| ZIP/Postal code |
01900 |
| Country |
Mexico |
| |
|
| Platform ID |
GPL3718 |
| Series (1) |
| GSE62407 |
Affymetrix SNP array data for lung cancer samples |
|
| Relations |
| Reanalyzed by |
GSE85838 |
