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.
- (WT/KO)-DRB3H --> Time zero of GRO-seq
- (WT/KO)-WASH10M --> 10 min after removing the blockage of PolII
- (WT/KO)-WASH20M --> 20 min after removing the blockage of PolII
- (WT/KO)-WASH30M --> 30 min after removing the blockage of PolII
- (WT/KO)-NODRB --> Reference for no blockage of PolII
The protocol is partially based on the original paper, updated based on Nagari et al.
Described in this document.
Selection of transcripts here
Generation of metagene profiles here
We prepared the figures for publication following this notebook