Help finding normal samples for DNA methylation on the 450K platform
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2.7 years ago
Lunky ▴ 30

Hello I'm looking for more DNA methylation normal samples. I currently have data from TCGA and GEO for breast, kidney, lung, and thyroid. More specifically, I have all the normal samples from TCGA and have looked at the GEO sets below:

#GSE79100: kidney 31 normal * missing key probes
#GSE88883: breast n=100 * too many missing values
#GSE37754: breast n=10 (Non-tumor)  * missing key probe
#GSE66313: breast n=15 (Adjacent-Normal)

Any recommendations would be appreciated.

Edit: looking for more kidney/renal normal samples on 450K platform, below are data I have already looked at in addition to above:

# GSE61441: kidney n=46 normal * no age data
450K methylation • 588 views
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One thing I have found useful is to look at papers describing methylation clocks, because they usually report public datasets which are of high quality. For example look at the GEOs described in this paper in their data availability section. Or the classic Horvath paper.

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