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Sample GSM8219206 Query DataSets for GSM8219206
Status Public on May 22, 2024
Title TC71_ITP
Sample type genomic
 
Source name genomic DNA from TC71_ITP
Organism Homo sapiens
Characteristics cell line: TC71
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_1
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]

Supplementary file Size Download File type/resource
GSM8219206_203923030020_R01C01_Grn.idat.gz 6.9 Mb (ftp)(http) IDAT
GSM8219206_203923030020_R01C01_Red.idat.gz 6.9 Mb (ftp)(http) IDAT

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