RNA-seq and histone modifictaion
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3.9 years ago
kanwarjag ★ 1.2k

If I have an RNA-seq data of control and treated samples. Can I estimate changes in H3K4me3, H3K27ac and H3K27me3 in embryonic stem cells from a public dataset? Which data set may be used to histone modification if we have expression data without doing ChIP-seq.

rna-seq • 882 views
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Does public datasets contain same treatment in histone modifications of chip seq data or knockout, knockin, knockdown of your histone writer rna seq data? If yes directly correlate. If not try seeing the expression of histone writers gene in your Rnaseq data. . Eg. Setdb1 or any other writer of H3K4me3, H3K27ac and H3K27me3. If they show alteration might be some effect. But without actually looking on histone chip seq for control and treatment it is difficult to conclude.

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3.9 years ago

You can peruse this database for your desired dataset: https://www.encodeproject.org/search/?type=Target

Also I've never used it before but I hear this is also a good place to look: https://deepblue.mpi-inf.mpg.de

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