|
| Status |
Public on Jun 19, 2015 |
| Title |
RT112_rep_2_copy_number_variation |
| Sample type |
genomic |
| |
|
| Source name |
Bladder Cell Line_RT112_rep_2
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: RT112_rep_2
cell type: bladder cancer
|
| Growth protocol |
Cells were cultured in RPMI supplemented with 10-20% FBS and were harvested at 70-90% confluence.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Extraction of genomic DNA using the DNAeasy blood and tissue kit (Qiagen)
|
| Label |
biotin
|
| Label protocol |
400ng of genomic DNA was whole-genome amplified, fragmented , precipitated and resuspended in hybridization buffer
|
| |
|
| Hybridization protocol |
Resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48ºC, single-base extension and allele-specific staining was performed on a Teflow chamber rack system.
|
| Scan protocol |
After allele-specific staining BeadChip arrays were scanned on a BeadArray Reader
|
| Description |
4399848624_R01C02
|
| Data processing |
Data processing was carried out with GenomeStudio software v2011.1 (Genotyping v1.9.4) provided by Illumina
Genotype: AA,AB,BB, or - - (no call)
GSE64572_cell_line_calls_with_annotation.txt: The Illumina 1 M Duo array includes 902,103 autosomal probes and 39,779 probes from sex chromosomes. A total of 43 different cell lines were hybridized to the arrays (GSE64572) Genotypes and R values were extracted using the beadstudio software (version 3.1.3.0) and R values were normalized using the method described by Pounds and co-workers. Log R ratios were calculated using as reference the average R value from 200 blood leukocyte samples from control subjects included in the EPICURO study with the R program version 2.8. Copy number calls were obtained using the waviCGH software. Gene copy number changes were called as follows: -1 = loss (hemi or homozygous), 0 = copy number neutral, 1 = gain.
|
| |
|
| Submission date |
Dec 30, 2014 |
| Last update date |
May 06, 2016 |
| Contact name |
Enrique Carrillo de Santa Pau |
| E-mail(s) |
enrique.carrillo@imdea.org
|
| Organization name |
Spanish National Cancer Research Centre (CNIO)
|
| Department |
Cancer Cell Biology Programme
|
| Lab |
Epithelial Carcinogenesis group
|
| Street address |
C/ Melchor Fernández Almagro, 3
|
| City |
Madrid |
| ZIP/Postal code |
28029 |
| Country |
Spain |
| |
|
| Platform ID |
GPL6984 |
| Series (2) |
| GSE64572 |
The UBC-40 Urothelial Bladder Cancer Cell Line Index [copy number variation] |
| GSE64573 |
The UBC-40 Urothelial Bladder Cancer Cell Line Index |
|
