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How to find Chip-seq and Methylome data to compare with my results?
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14 months ago
Expert • 30

Hi there,

I am working on a set of microarray data set from conversion of MEF to iCM. in my own workflow, I found a set of DEGs and target TFs and histones and now I am looking for ChIP-seq and methylome data to compare with my results. so my question is, How can I find these kinds of data in NCBI or other data repositories for iCM data? I don't want to have raw data as we see in some studies, I only want to visualize others finding in IGB or even UCSC to compare with my findings. and as you know IGB can visualize specific formats, not raw data.

Thanks in advance

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Have you tried to look into databases like GEO? That's what I normally do, and I usually look for datasets that are published to have additional information. I am not really sure there are any shortcuts to this process. The only catch is that not all repositories may have the processed data in the form you want (e.g.: bedGraph file of the results etc...), but they could. You will have to search for one that matches what you want I think.

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You can search ENCODE db for your specific cell type.

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