Illumina Infinium Methylation 450K Demo Data
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8.4 years ago
ugoodlfy ▴ 30

Hello guys, I need some illumina Infinium Methylation 450K demo data to play. I have search online for a long time , but can only find some tools like IMA(Illumina Methylation Analyzer) and methylumi etc. Is anybody know some databases provide illumina Infinium Methylation 450K demo data ? Thanks a lot .

methylation illumina • 5.0k views
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8.4 years ago
Neilfws 49k

There is publicly-available 450K data in The Cancer Genome Atlas (TCGA).

It's a little difficult to navigate for new users. I would start with the data matrix and select, for example COAD (colon adenocarcinoma), then DNA Methylation under Data Type. You should then see JHU_USC HumanMethylation450 under Center/Platform.

There's also direct FTP access; here's the COAD 450K directory.

You'll need to spend some time reading the TCGA documentation to figure out their barcode system.

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8.4 years ago

As of today, it appears that 2215 samples have been assayed on the illumina 450k platform at NCBI GEO.

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Incredible: I ran a search of platforms there yesterday using "450K" as query, nothing came up. Today, search will not even complete (returns an error). Search/retrieval at GEO is just appalling.

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Do report your problems to <geo at="" ncbi.nlm.nih.gov="">. They have typically been responsive when I have found errors and other major problems.

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That is because the official platform name is Illumina HumanMethylation450 BeadChip. The K would make it not match.

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Good search algorithms would account for that and return nearest matches. "HumanMethylation" returns no results, "HumanMethylation450" does. This is just poor search implementation.

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