Arabidopsis_H3K4me1

Codes used for 'Transcription-coupled and epigenome-encoded mechanisms direct H3K4 methylation (2022)'

for codes for Supplementary Figure.5, please see Figure2 and 3.r

for codes for Supplementary Figure 9,10,11, please see Figure4.r

update 2024.01.11

Upon multiple requests, we added the following list of genes in data/list_of_genes folder.

• ATX1/2/R7-marked genes
• ATX3/4/5-marked genes
• ATXR3-marked genes
• ATX1-bound genes
• ATX2-bound genes
• ATXR7-bound genes

As a note for reproducibility, those lists can also be generated (as R object) by running Figure1.R L58- for ATX-marked genes, and by Supplementary_Figure3.R L8- for ATX-bound genes.

• Are you looking for the formatted data table behind scatter plot of Figure1. d? Please use data/Figure1/ChIP1_RPKM.txt and data/Figure1/ChIP1_RPM.txt.
• Are you looking for browser tracks? Sorry, we didn't upload them in GEO nor here (we might in future)- tell us (soya[at]ucdavis.edu) what you need and we'll email you.

Can't find what you are looking for? Pardon my bad code annotation! Please ask us via "Issues" section of GitHub or contact soya[at]ucdavis.edu ;)