|
| Status |
Public on Dec 19, 2023 |
| Title |
RMS2_O_P17* [methylation] |
| Sample type |
genomic |
| |
|
| Source name |
RMS2 organoid
|
| Organism |
Homo sapiens |
| Characteristics |
cell_type: Rhabdomyosarcoma
age_in_years: 7
Sex: M
histological_subtype: Embryonal
disease_state: Relapse/metastatic
sample_location: Lung
primary_tumor_location: Ischioanal
fresh/cryopreserved: cryopreserved
medium: M3
passage_number: P17
culture_type: 3D
|
| Growth protocol |
Culture medium was changed twice a week, and RMS_O were split every 2 weeks on average. Finally, culture medium was changed 24 to 48 h before extraction.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
genomic DNA (gDNA) from both RMS tissues and matched in vitro models cultured in 2D or 3D conditions with DMEM, M3 and M5 media were extracted using the Allprep DNA/RNA/miRNA universal kit (Qiagen, cat. no. 80224), following manufacturer’s instructions.
|
| Label |
Cy3 and Cy5
|
| Label protocol |
100 to 500 ng of gDNA was hybridized to Illumina Infinium HumanMethylationEPIC BeadChip (850K) arrays at the International Agency for Research on Cancer (IARC), in collaboration with the team of Z. Herceg (IARC, Lyon), according to the manufacturer’s protocol recommendations.
|
| |
|
| Hybridization protocol |
100 to 500 ng of gDNA was hybridized to Illumina Infinium HumanMethylationEPIC BeadChip (850K) arrays at the International Agency for Research on Cancer (IARC), in collaboration with the team of Z. Herceg (IARC, Lyon), according to the manufacturer’s protocol recommendations.
|
| Scan protocol |
100 to 500 ng of gDNA was hybridized to Illumina Infinium HumanMethylationEPIC BeadChip (850K) arrays at the International Agency for Research on Cancer (IARC), in collaboration with the team of Z. Herceg (IARC, Lyon), according to the manufacturer’s protocol recommendations.
|
| Data processing |
Methylation data were analyzed using minfi (R library v.1.44.0). Normalization was performed for all samples using functional normalization (FunNorm) with default parameters. Filtering was performed to remove (1) poor performing probes, i.e. detection p-value above 0.01 in one or more samples, (2) probes located on sex chromosomes, (3) probes known to have common SNPs at the CpG site using dropLociWithSnps function; and (4) cross-reactive probes published by Chen et al. (2013) and Pidsley et al. (2016). Beta values were extracted using the getBeta function from minfi with default parameters.
|
| |
|
| Submission date |
Nov 17, 2023 |
| Last update date |
Dec 19, 2023 |
| Contact name |
Thomas Diot |
| Organization name |
Cancer Research Center of Lyon
|
| Street address |
28 Rue Laennec
|
| City |
Lyon |
| ZIP/Postal code |
69008 |
| Country |
France |
| |
|
| Platform ID |
GPL21145 |
| Series (2) |
| GSE248182 |
Modeling the next-generation of rhabdomyosarcoma organoids to predict effective drug combinations [methylation] |
| GSE248183 |
Modeling the next-generation of rhabdomyosarcoma organoids to predict effective drug combinations |
|
