|
| Status |
Public on Jul 06, 2021 |
| Title |
RB301 (SNP_370K) |
| Sample type |
genomic |
| |
|
| Source name |
retinblastoma sample RB301
|
| Organism |
Homo sapiens |
| Characteristics |
geo dataset: SAMPLE 84
batch name: PJ090106
tissue: retinoblastoma
|
| Treatment protocol |
NA
|
| Growth protocol |
NA
|
| 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 |
Cy5
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
Standard Illumina Protocol
|
| Scan protocol |
Standard Illumina Protocol
|
| Description |
SNP array data from retinoblastoma samples
Data_370k_processed.RData
Data_370k_raw.RData
processed_data_i_GPL6985_retino_all_samples.csv
raw_data_i_GPL6985_retino_all_samples.csv
Sample name in the .csv files: SAMPLE 39
|
| Data processing |
The B allele frequency and log-ratio signals were smoothes and analyzed using the Geneome Alteration Print (GAP) algorithm (Popova et al., 2009).
1.Raw data file :
X raw and Y raw : raw coordinates ; X and Y: normalized coordinates
1.Processed data file :
score: GenomeStudio score; Theta: GenomeStudio genotype metric; R: GenomeStudio intensity metric; B allele frequency: GenomeStudio B allele frequency estimate; Log R ratio: GenomeStudio signal intensity estimate
|
| |
|
| 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 |
GPL6985 |
| Series (2) |
| GSE58781 |
Retinoblastoma SNP array data |
| GSE58785 |
Pan-genomic study of primary human retinoblastoma samples |
|
