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| Status |
Public on Apr 04, 2017 |
| Title |
Assessing the clear cell Renal Cell Carcinoma (ccRCC) DNA-methylome by MethylCapSeq |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by high throughput sequencing
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| Summary |
MethylCap-Seq experiments of 4 ccRCC cell lines (SKRC1, SKRC10, SKRC52, SKRC59) and one "normal" kidney cell line (HK2) were performed, and used, in combination with DAC/TSA re-expression data, to mine the ccRCC specific cancer methylome. Identified candidate DNA-methylation markers were evaluated by MSP in two independent series, yielding 4 validated markers (GREM1, NEURL, LAD1, NEFH) of which promoter methylation was highly predictive of survival.
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| Overall design |
After enrichment of methylated DNA by MBD-based affinity purification, captured fragments were paired-end sequenced on the GAIIx.
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| Contributor(s) |
Vlodrop IJ, De Meyer T, Smits KM, Van Neste L, Baldewijns MM, Moerkerk PT, Schouten LJ, van den Brandt PA, Mi Yi J, Jeschke J, de Freitas Calmon M, Schuebel KE, Ahuja N, Baylin SB, Herman JG, Soetekouw P, Bosman FT, Van Criekinge W, Van Engeland M |
| Citation(s) |
27756787 |
| Submission date |
Nov 25, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Tim De Meyer |
| Organization name |
Ghent University
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| Department |
Dept. of Mathematical Modelling, Statistics and Bioinformatics
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| Lab |
BIOBIX lab of Bioinformatics and Computational Genomics
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| Street address |
Coupure Links 653
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| City |
Ghent |
| ZIP/Postal code |
9000 |
| Country |
Belgium |
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| Platforms (1) |
| GPL10999 |
Illumina Genome Analyzer IIx (Homo sapiens) |
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| Samples (5)
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| Relations |
| SRA |
SRP009473 |
| BioProject |
PRJNA150547 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE33954_RAW.tar |
758.1 Mb |
(http)(custom) |
TAR (of BOWTIE) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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