|
| Status |
Public on Mar 20, 2012 |
| Title |
SNU-886 |
| Sample type |
genomic |
| |
|
| Source name |
KCLB
|
| Organism |
Homo sapiens |
| Characteristics |
primary site: liver
histology: carcinoma
histology subtype1: hepatocellular_carcinoma
|
| Treatment protocol |
None
|
| Growth protocol |
Cells lines were cultured following growth recommendations from the cell line source vendors. Cells were incubated at 37 ºC at 5% CO2 until 70% confluency was reached. Pellets were harvested 48 hours post media change, flash frozen, and stored at -80 ºC until nucleic acid extraction.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from frozen cell pellets, containing an average cell count of 4.5 million cells, using the Qiagen Gentra Puregene method following the manufacturers recommendations. Samples were quantified using picogreen on a ThermoScientific Varioskan Flash instrument.
|
| Label |
Biotin
|
| Label protocol |
PCR amplification fragments (200 and 1100 bp) are labeled using terminal deoxynucleotidyl transferase following the Affymetrix GenomeWideSNP_6 protocol
|
| |
|
| Hybridization protocol |
After denaturation, 200ul of sample are injected into a Genome-Wide Human SNP 6.0 array. Arrays are loaded in the GeneChip® Hybridization Oven 640 @ 50 °C temp, rotating arrays @ 60 rpm. Samples are hybridized for 16 to 18 hours.
|
| Scan protocol |
Genome-Wide Human SNP Array 6.0 are stained using the GeneChip® Fluidics Station 450 and scanned using the GeneChip® Scanner 3000
|
| Description |
SNP array data from the CCLE
|
| Data processing |
The raw CEL files were normalized to copy number estimates using a GenePattern pipeline, as described in Cancer Genome Atlas Research Network et al, Nature, 2008, and hg18 Affymetrix probe annotations. Normalized copy number estimates (log2 ratios) were segmented using the Circular Binary Segmentation (CBS) algorithm, followed by median centering of the segment values to a value of zero in each sample.
|
| |
|
| Submission date |
Mar 06, 2012 |
| Last update date |
Oct 30, 2013 |
| Contact name |
Nicolas Stransky |
| E-mail(s) |
[email protected]
|
| URL |
http://www.broadinstitute.org/ccle
|
| Organization name |
Broad Institute
|
| Department |
Cancer Program
|
| Lab |
Levi Garraway
|
| Street address |
7 Cambridge center
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02118 |
| Country |
USA |
| |
|
| Platform ID |
GPL15315 |
| Series (2) |
| GSE36138 |
SNP array data from the Cancer Cell Line Encyclopedia (CCLE) |
| GSE36139 |
SNP and Expression data from the Cancer Cell Line Encyclopedia (CCLE) |
|
| Relations |
| Reanalyzed by |
GSE51798 |
