|
| Status |
Public on Sep 21, 2012 |
| Title |
Cell Line H1836 |
| Sample type |
genomic |
| |
|
| Source name |
Small Cell Lung Cancer
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Small Cell Lung Cancer
cell line: H1836
|
| Treatment protocol |
Cells were not treated before DNA extraction
|
| Growth protocol |
Cell lines were grown according to standard conditions (RPMI and HITES Medium supplemented with 10% FCS).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from cell lines using the Gentra PureGene kit (Qiagen) following manufacturer’s instructions and quantified using PicoGreen.
|
| Label |
biotin
|
| Label protocol |
as per manufacturer
|
| |
|
| Hybridization protocol |
according to the manufacturer's instructions DNA was hybridized to Affymetrix SNP Arrays 6.0
|
| Scan protocol |
arrays were washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
|
| Description |
hybridized to 6.0 SNP arrays
|
| Data processing |
CEL files, TXT and SEG files. SEG Files were created from CEL files by SNPFileCreator (Genepattern, Broad Institute). SEG files (.seg) list loci and associated numeric copy number values as tab delimited text files. The first row contains column headings. Next, copy numbers were determined by using IGV 2.1 Software (Genepattern, Broad Institute). IGV reads the first four columns as track name, chromosome, start location, and end location and the last column as the numeric value for that locus. The numeric copy number value was then determined as the inferred copy number from IGV 2.1 for each sample separately.
|
| |
|
| Submission date |
Aug 15, 2012 |
| Last update date |
Sep 21, 2012 |
| Contact name |
Felix Dietlein |
| Organization name |
University of Cologne
|
| Department |
Department of Translational Genomics
|
| Street address |
Weyertal 115b
|
| City |
Cologne |
| State/province |
NRW |
| ZIP/Postal code |
50931 |
| Country |
Germany |
| |
|
| Platform ID |
GPL6801 |
| Series (1) |
| GSE40142 |
A framework for identification of actionable cancer genome dependencies in small cell lung cancer |
|
