|
| Status |
Public on Sep 20, 2023 |
| Title |
primary ATRT, ATRT23 |
| Sample type |
genomic |
| |
|
| Source name |
primary tumor
|
| Organism |
Homo sapiens |
| Characteristics |
anatomic location: Basal Ganglia
age at diagnosis: 2.3
|
| Treatment protocol |
please refer to GEO:GSE175892
|
| Growth protocol |
please refer to GEO:GSE175892
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
please refer to GEO:GSE175892
|
| Label |
cy3, cy5
|
| Label protocol |
please refer to GEO:GSE175892
|
| |
|
| Hybridization protocol |
please refer to GEO:GSE175892
|
| Scan protocol |
please refer to GEO:GSE175892
|
| Data processing |
Re-analysis: RnBeads Bioconductor R package version 1.6.1 (Assenov et al., 2014; doi: 10.1038/nmeth.3115) was used to re-process the data from IDAT files. All samples and all probes were kept after quality control. Probe intensities were normalized using the rnb.execute.normalization() function with the “illumina” method. Probes outside CpG context (2991 probes), targeting single nucleotide polymorphisms (17369 probes) or targeting X and Y chromosomes (19457 probes) were respectively filtered out before subsequent analysis.
beta-value; processed file matrix in a separate file: matrix_LobonIglesias2023_DNAmethylation_EPICarray_reanalysed_primaryATRT.csv; sample ID correspondance with Andrianteranagna et al., 2021 paper is given in a separate file: LobonIglesias2023_Andrianteranagna2021_sampleIDs.csv
|
| |
|
| Submission date |
Aug 31, 2023 |
| Last update date |
Sep 20, 2023 |
| Contact name |
Mamy Jean de Dieu ANDRIANTERANAGNA |
| E-mail(s) |
mamy-jean-de-dieu.andrianteranagna@curie.fr
|
| Phone |
+33156246274
|
| Organization name |
Institut Curie
|
| Department |
Centre de Recherche
|
| Lab |
U900
|
| Street address |
26 rue d'Ulm
|
| City |
Paris |
| State/province |
Ile de France |
| ZIP/Postal code |
75005 |
| Country |
France |
| |
|
| Platform ID |
GPL21145 |
| Series (2) |
| GSE242089 |
Imaging and multi-omics datasets converge to define different neural progenitor origins for ATRT-SHH subgroups [DNAmeth_EPICarray] |
| GSE242090 |
Imaging and multi-omics datasets converge to define different neural progenitor origins for ATRT-SHH subgroups |
|
