|
| Status |
Public on Jul 06, 2021 |
| Title |
RBsjd3 (SNP_CytoScan) |
| Sample type |
genomic |
| |
|
| Source name |
retinoblastoma sample RBsjd3
|
| Organism |
Homo sapiens |
| Characteristics |
geo dataset serie: SAMPLE 112
tissue: retinoblastoma
|
| Growth protocol |
Immediately following enucleation, a needle was inserted through the anterior chamber of the eye to extract a tumor sample by aspiration. The tumor specimen was placed in RPMI medium on ice, cells were re-suspended, counted and separated into two tubes (for DNA and RNA preparation). The tubes were then centrifuged to remove all media and snap frozen for later extraction.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For DNA extraction, samples were first incubated in a lysis buffer with proteinase K, recombinant. They were next incubated with RNAse A. DNA was then extracted using a standard phenol-chloroform protocol
|
| 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 |
SNP array data from retinoblastoma samples
|
| Data processing |
SNP arrays were analyzed using the Genome Alteration Print method71 (Popova et al., 2009), which takes into account both the log ratio and B allele frequency signals to determine normal cell contamination, tumor ploidy and the absolute copy-number of each segment.
CN : Copy Number, BA : B allete Frequency
|
| |
|
| Submission date |
Mar 01, 2021 |
| Last update date |
Jul 06, 2021 |
| Contact name |
Elodie chapeaublanc |
| E-mail(s) |
elodie.chapeaublanc@pasteur.fr
|
| Organization name |
Institut Curie
|
| Department |
UMR 144
|
| Lab |
Equipe Radvanyi
|
| Street address |
26 rue d'ulm
|
| City |
paris |
| ZIP/Postal code |
75248 |
| Country |
France |
| |
|
| Platform ID |
GPL16131 |
| Series (2) |
| GSE58781 |
Retinoblastoma SNP array data |
| GSE58785 |
Pan-genomic study of primary human retinoblastoma samples |
|
