RNA-seq and histone modifictaion
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.
• 1,449 views
•
link
updated
by
science_lizard •
•
written
by
kanwarjag
•
written
by
kanwarjag
1 answer
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
• 0 views
•
link
written
by
science_lizard •
Log in to answer this question.
More posts like this
-
Public data to investigate gene regulatory network
written by Shicheng Guo
-
Identifying differential histone mark (H3k27me3 and H3k4me3) in treated and control sample
written by munaj86 •
-
Chip-seq data of bivalent regions in hESC
written by chipolino •
-
Expected correlation between ATAC data and Chip-Seq histone marks
written by bipin •
-
Does H3K27ac generate narrow or broad peaks?
written by jklopp •
-
Histone modifications data on embryonic stem cells to differentiated stages
written by Chirag Nepal
-
looking for chip-seq histone marks and rna-seq data
written by tonja.r
-
histone methylation public database
written by kanwarjag
-
unite histone sites, DNAse, Chip-seq data from different cell types.
written by tonja.r
-
SNPs in DNase hypersensitive and histone marks sites
written by tonja.r
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.