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| Status |
Public on Jul 06, 2021 |
| Title |
Retinoblastoma SNP array data |
| Organism |
Homo sapiens |
| Experiment type |
Genome variation profiling by SNP array
|
| Summary |
Retinoblastoma is the most common intraocular cancer of infancy and childhood, with an incidence of one case per 15,000 - 20,000 live births. An early event in retinoblastoma genesis is a functional loss of both alleles of the RB1 gene. However, other genes are likely to be involved in the development of this cancer. In this study we sought to build a comprehensive molecular portrait of this cancer by performing transcriptomic, methylomic, genomic profiling of primary retinoblastoma samples. Most of the patients whose tumors were studied had received no treatment prior to surgical enucleation.
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| Overall design |
Immediately following enucleation, a needle was inserted through the eye?s anterior chamber to extract a tumor sample by aspiration; the tumor specimen was then snap frozen. For these arrays, DNA was extracted from these snap frozen samples.
We used Affymetrix CytoScan HD Array arrays to study the genome alteration patterns of 28 primary retinoblastoma tumors
We used Illumina 370K SNP arrays to study the genome alteration patterns of 44 primary retinoblastoma tumors
We used Illumina 610 0K SNP arrays to study the genome alteration patterns of 22 primary retinoblastoma tumors
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| Contributor(s) |
Radvanyi F, Sefta M, Liu J, Chapeaublanc E, Desbrousses C, Ottaviani D |
| Citation(s) |
34552068 |
| Submission date |
Jun 24, 2014 |
| Last update date |
Sep 24, 2021 |
| Contact name |
Elodie chapeaublanc |
| E-mail(s) |
elodie.chapeaublanc@pasteur.fr
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| Organization name |
Institut Curie
|
| Department |
UMR 144
|
| Lab |
Equipe Radvanyi
|
| Street address |
26 rue d'ulm
|
| City |
paris |
| ZIP/Postal code |
75248 |
| Country |
France |
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| Platforms (3) |
| GPL6985 |
Illumina HumanCNV370-QuadV3 DNA Analysis BeadChip (HumanCNV370-QuadV3_C) |
| GPL8887 |
Illumina Human610-Quad v1.0 BeadChip |
| GPL16131 |
[CytoScanHD_Array] Affymetrix CytoScan HD Array |
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| Samples (94)
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| This SubSeries is part of SuperSeries: |
| GSE58785 |
Pan-genomic study of primary human retinoblastoma samples |
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| Relations |
| BioProject |
PRJNA253484 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE58781_Data_370k_processed.RData.gz |
339.0 Mb |
(ftp)(http) |
RDATA |
| GSE58781_Data_370k_raw.RData.gz |
220.1 Mb |
(ftp)(http) |
RDATA |
| GSE58781_RAW.tar |
1.2 Gb |
(http)(custom) |
TAR (of CEL, CSV, IDAT) |
| GSE58781_data_proc_610k.RData.gz |
281.5 Mb |
(ftp)(http) |
RDATA |
| GSE58781_data_raw_610k.RData.gz |
191.5 Mb |
(ftp)(http) |
RDATA |
| GSE58781_processed_data_i_GPL6985_retino_all_samples.csv.gz |
295.7 Mb |
(ftp)(http) |
CSV |
| GSE58781_processed_data_i_GPL8887_retino_all_samples.csv.gz |
246.8 Mb |
(ftp)(http) |
CSV |
| GSE58781_raw_data_i_GPL6985_retino_all_samples.csv.gz |
216.6 Mb |
(ftp)(http) |
CSV |
| GSE58781_raw_data_i_GPL8887_retino_all_samples.csv.gz |
191.9 Mb |
(ftp)(http) |
CSV |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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