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Hi
We are currently using PolII ChIP-seq for expression analysis, but find that there are some disadvantages (low sensitivity etc.). This could probably to some extent be solved by deeper sequencing, but due to costs, we would prefer not to do that. So we are considering mRNA-seq; does anyone know how much coverage you need if you only want to look at expression levels and not splice variants etc. Has anyone compared the two techniques? One thing that we like about PolII-ChIPseq is the fact that you get a more direct measurement of transcriptional activity compared to mRNA-seq or microarray which are also affected by mRNA stability. However, it should be possible to look at intron levels in mRNA-seq and get similar information. Has anyone tried that, and if so, which coverage is needed?
Thanks
Søren
We are currently using PolII ChIP-seq for expression analysis, but find that there are some disadvantages (low sensitivity etc.). This could probably to some extent be solved by deeper sequencing, but due to costs, we would prefer not to do that. So we are considering mRNA-seq; does anyone know how much coverage you need if you only want to look at expression levels and not splice variants etc. Has anyone compared the two techniques? One thing that we like about PolII-ChIPseq is the fact that you get a more direct measurement of transcriptional activity compared to mRNA-seq or microarray which are also affected by mRNA stability. However, it should be possible to look at intron levels in mRNA-seq and get similar information. Has anyone tried that, and if so, which coverage is needed?
Thanks
Søren