|
| Status |
Public on Jul 06, 2021 |
| Title |
RB42_REP2 (expression) |
| Sample type |
RNA |
| |
|
| Source name |
retinoblastoma sample RB42_REP2
|
| Organism |
Homo sapiens |
| Characteristics |
geo dataset serie: SAMPLE 33
batch: RT09
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 |
total RNA |
| Extraction protocol |
Tumor RNA was extracted using Qiazol (Qiagen, Courtaboeuf, France) according to the manufacturer instructions and purified using miRNeasy Mini kit (Qiagen).
|
| Label |
biotin
|
| Label protocol |
100ng of total RNA were amplified to produced biotinylated complementary RNAs, as recommended by Affymetrix.
|
| |
|
| Hybridization protocol |
Affymetrix microarrays were hybridized with 10µg of biotinylated cRNA according the supplier recommendations. Microarrays were washed and stained using FS450 fluidics upon a protocol provided by Affymetrix, corresponding to the U133plus 2.0 arrays
|
| Scan protocol |
Microarrays were scanned using a 7G, Affymetrix GCS3000 scanner, raw data were acquired with Affymetrix Genechip Command Console.
|
| Description |
Batch replicate - Gene expression data from retinoblastoma samples
|
| Data processing |
Signal reconstruction was performed with the RMA algorithm as implemented in Bioconductor affy package on R statistical software using the Dai custom CDF package: HGU133Plus2_Hs_ENTREZG, Brainarray Custom CDF EntrezG version 23, Batch effects were corrected with the help of the bioconductor package SVA,
|
| |
|
| 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 |
GPL28718 |
| Series (2) |
| GSE58780 |
Retinoblastoma gene expression data |
| GSE58785 |
Pan-genomic study of primary human retinoblastoma samples |
|
