|
| Status |
Public on May 22, 2024 |
| Title |
A673 UTA_ITP_1 |
| Sample type |
genomic |
| |
|
| Source name |
genomic DNA from A673 UTA_ITP_1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A673
disease state: Ewing_sarcoma
|
| Treatment protocol |
Not applicable.
|
| Growth protocol |
All cell lines were cultured at 37 °C, 5% CO2 in RPMI 1640 (Biochrom, Germany) supplemented with 10% fetal bovine serum (Sigma-Aldrich, Germany) and 1% penicillin-streptomycin (Merck, Germany).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
When flasks reached approximately 70% confluency, samples were lysed, and total DNA was extracted with the NucleoSpin Tissue kit (Macherey Nagel) following the manufacturer’s protocol.
|
| Label |
cy3 and cy5
|
| Label protocol |
cy3, cy5
|
| |
|
| Hybridization protocol |
DNA was bisulfite converted, amplified, fragmented, and hybridised to Illumina Infinium MethylationEPIC BeadChip arrays following manufacturer's protocol
|
| Scan protocol |
Illumina protocol
|
| Description |
Replicate_2
|
| Data processing |
The initial pre-processing of the raw methylation was performed in R version 3.3.1. Raw signal intensities were obtained from IDAT-files using the minfi Bioconductor package version 1.21.4 in R version 3.3.1. Each sample was individually normalized by performing a background correction (shifting of the 5% percentile of negative control probe intensities to 0) and a dye-bias correction (scaling the mean of normalization control probe intensities to 10,000) for both color channels. The methylated and unmethylated signals were corrected individually. Subsequently, beta values were calculated from the retransformed intensities using an offset of 100 (as recommended by Illumina). Out of 865,859 probes on the EPIC array, 105,454 probes were masked according to Zhou et al. as well as 16,944 probes on the X and Y chromosomes. In total, 743,461 probes were kept for downstream analysis. The beta values were transformed to M-values with the logit2 function of the minfi package version 1.42.0, R version 4.2.0.
processed data file contains: Average Beta
|
| |
|
| Submission date |
Apr 21, 2024 |
| Last update date |
May 22, 2024 |
| Contact name |
Thomas Georg Philipp Grunewald |
| E-mail(s) |
t.gruenewald@kitz-heidelberg.de
|
| Phone |
0049-6221-423718
|
| Organization name |
German Cancer Research Center (DKFZ)
|
| Department |
Division of Translational Pediatric Sarcoma Research
|
| Street address |
Im Neuenheimer Feld 280
|
| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21145 |
| Series (1) |
| GSE264509 |
Genomic and phenotypic stability of fusion-driven pediatric sarcoma cell lines [array] |
|
