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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 03, 2024 |
| Title |
Sample_556 |
| Sample type |
genomic |
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| Source name |
Lymph_node
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| Organism |
Homo sapiens |
| Characteristics |
response_to_ici: R
localisation: LN
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA (gDNA) was extracted using the Maxwell FFPE Plus Kit (Promega, Madison, Wisconsin, USA).
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| Label |
cy3, cy5
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| Label protocol |
500ng of gDNA was sodium bisulfite converted using the EpiTect Fast DNA Bisulfite Kit (Qiagen, Germantown, MD, USA), processed using the Infinium HD FFPE DNA Restore Kit (Illumina, San Diego, CA, USA) and processed for microarray hybridization using Infinium MethylationEPIC Kit.
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| Hybridization protocol |
Sodium bisulfite treated gDNA was amplified and enzymatically fragmented before hybridization to the microarray. After washing and staining, the microarray was scanned using the iScan device (Illumina).
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| Scan protocol |
Infinium MethylationEPIC microarray platform
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| Data processing |
Raw red/green channel *.idat files were imported into R using the RnBeads packages for initial quality control, data normalization (SWAN) and extraction of β-values representing the percentage of methylation for each CpG site on the microarray. SNP-enriched, cross-reactive, non-CpG and sex chromosome specific probes were removed from further analyses. Differential methylation was calculated using limma and RnBead´s rank cutoff. The top 500 differentially methylated CpG sites were used for further analyses.
Normalized Average Beta
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| Submission date |
Jun 16, 2023 |
| Last update date |
Apr 03, 2024 |
| Contact name |
Gerwin Heller |
| E-mail(s) |
gerwin.heller@meduniwien.ac.at
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| Organization name |
Medical University of Vienna
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| Department |
Medicine I
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| Street address |
Währinger Gürtel 18-20
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| City |
Wien |
| ZIP/Postal code |
1090 |
| Country |
Austria |
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| Platform ID |
GPL23976 |
| Series (1) |
| GSE235122 |
DNA methylation signatures correlate with response to immune checkpoint inhibitors in metastatic melanoma |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSM7495522_205828610168_R08C01_Grn.idat.gz |
7.1 Mb |
(ftp)(http) |
IDAT |
| GSM7495522_205828610168_R08C01_Red.idat.gz |
7.2 Mb |
(ftp)(http) |
IDAT |
| Processed data are available on Series record |
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