Groseq_mESC.md

Analysis of Pol-II activity (GRO-seq) in mouse ESC in connection to 5fC

The raw data has been taken from Wang et al., Nature 2015

The GEO for the GRO-seq data is GSE64748. There are 5 datasets (with duplicates) for WT and for TDG-KO.

1. (WT/KO)-DRB3H --> Time zero of GRO-seq
2. (WT/KO)-WASH10M --> 10 min after removing the blockage of PolII
3. (WT/KO)-WASH20M --> 20 min after removing the blockage of PolII
4. (WT/KO)-WASH30M --> 30 min after removing the blockage of PolII
5. (WT/KO)-NODRB --> Reference for no blockage of PolII

The protocol is partially based on the original paper, updated based on Nagari et al.

Obtain raw data, perform trimming, alignment and conversion to BigWig format.

Described in this document.

Select transcripts for the metagene analysis, and perform the analysis

Selection of transcripts here

Generation of metagene profiles here

Plot results

We prepared the figures for publication following this notebook